diff --git a/Data/Sys/Wii/shared2/sys/SYSCONF b/Data/Sys/Wii/shared2/sys/SYSCONF
deleted file mode 100644
index 283c84a7e4..0000000000
Binary files a/Data/Sys/Wii/shared2/sys/SYSCONF and /dev/null differ
diff --git a/Source/Core/Common/NandPaths.cpp b/Source/Core/Common/NandPaths.cpp
index 60cb49fa26..99c75f01f8 100644
--- a/Source/Core/Common/NandPaths.cpp
+++ b/Source/Core/Common/NandPaths.cpp
@@ -20,46 +20,7 @@
 
 namespace Common
 {
-static std::string s_temp_wii_root;
-
-void InitializeWiiRoot(bool use_dummy)
-{
-  ShutdownWiiRoot();
-  if (use_dummy)
-  {
-    s_temp_wii_root = File::CreateTempDir();
-    if (s_temp_wii_root.empty())
-    {
-      ERROR_LOG(WII_IPC_FILEIO, "Could not create temporary directory");
-      return;
-    }
-    File::CopyDir(File::GetSysDirectory() + WII_USER_DIR, s_temp_wii_root);
-    WARN_LOG(WII_IPC_FILEIO, "Using temporary directory %s for minimal Wii FS",
-             s_temp_wii_root.c_str());
-    static bool s_registered;
-    if (!s_registered)
-    {
-      s_registered = true;
-      atexit(ShutdownWiiRoot);
-    }
-    File::SetUserPath(D_SESSION_WIIROOT_IDX, s_temp_wii_root);
-  }
-  else
-  {
-    File::SetUserPath(D_SESSION_WIIROOT_IDX, File::GetUserPath(D_WIIROOT_IDX));
-  }
-}
-
-void ShutdownWiiRoot()
-{
-  if (!s_temp_wii_root.empty())
-  {
-    File::DeleteDirRecursively(s_temp_wii_root);
-    s_temp_wii_root.clear();
-  }
-}
-
-static std::string RootUserPath(FromWhichRoot from)
+std::string RootUserPath(FromWhichRoot from)
 {
   int idx = from == FROM_CONFIGURED_ROOT ? D_WIIROOT_IDX : D_SESSION_WIIROOT_IDX;
   return File::GetUserPath(idx);
diff --git a/Source/Core/Common/NandPaths.h b/Source/Core/Common/NandPaths.h
index ab15d6f049..c5a3234e8c 100644
--- a/Source/Core/Common/NandPaths.h
+++ b/Source/Core/Common/NandPaths.h
@@ -15,15 +15,13 @@ static const std::string TITLEID_SYSMENU_STRING = "0000000100000002";
 
 namespace Common
 {
-void InitializeWiiRoot(bool use_temporary);
-void ShutdownWiiRoot();
-
 enum FromWhichRoot
 {
   FROM_CONFIGURED_ROOT,  // not related to currently running game - use D_WIIROOT_IDX
   FROM_SESSION_ROOT,     // request from currently running game - use D_SESSION_WIIROOT_IDX
 };
 
+std::string RootUserPath(FromWhichRoot from);
 std::string GetTicketFileName(u64 _titleID, FromWhichRoot from);
 std::string GetTMDFileName(u64 _titleID, FromWhichRoot from);
 std::string GetTitleDataPath(u64 _titleID, FromWhichRoot from);
diff --git a/Source/Core/Common/SysConf.cpp b/Source/Core/Common/SysConf.cpp
index 3b2ab36694..e8f8fb3cef 100644
--- a/Source/Core/Common/SysConf.cpp
+++ b/Source/Core/Common/SysConf.cpp
@@ -17,9 +17,9 @@
 
 #include "Core/Movie.h"
 
-SysConf::SysConf()
+SysConf::SysConf(const Common::FromWhichRoot root_type)
 {
-  UpdateLocation();
+  UpdateLocation(root_type);
 }
 
 SysConf::~SysConf()
@@ -50,6 +50,7 @@ bool SysConf::LoadFromFile(const std::string& filename)
   {
     File::CreateFullPath(filename);
     GenerateSysConf();
+    ApplySettingsFromMovie();
     return true;
   }
 
@@ -61,12 +62,10 @@ bool SysConf::LoadFromFile(const std::string& filename)
                   SYSCONF_SIZE, size))
     {
       GenerateSysConf();
+      ApplySettingsFromMovie();
       return true;
     }
-    else
-    {
-      return false;
-    }
+    return false;
   }
 
   File::IOFile f(filename, "rb");
@@ -76,13 +75,7 @@ bool SysConf::LoadFromFile(const std::string& filename)
     {
       m_Filename = filename;
       m_IsValid = true;
-      // Apply Wii settings from normal SYSCONF on Movie recording/playback
-      if (Movie::IsRecordingInput() || Movie::IsPlayingInput())
-      {
-        SetData("IPL.LNG", Movie::GetLanguage());
-        SetData("IPL.E60", Movie::IsPAL60());
-        SetData("IPL.PGS", Movie::IsProgressive());
-      }
+      ApplySettingsFromMovie();
       return true;
     }
   }
@@ -90,6 +83,17 @@ bool SysConf::LoadFromFile(const std::string& filename)
   return false;
 }
 
+// Apply Wii settings from normal SYSCONF on Movie recording/playback
+void SysConf::ApplySettingsFromMovie()
+{
+  if (!Movie::IsMovieActive())
+    return;
+
+  SetData("IPL.LNG", Movie::GetLanguage());
+  SetData("IPL.E60", Movie::IsPAL60());
+  SetData("IPL.PGS", Movie::IsProgressive());
+}
+
 bool SysConf::LoadFromFileInternal(File::IOFile&& file)
 {
   // Fill in infos
@@ -420,7 +424,7 @@ bool SysConf::Save()
   return SaveToFile(m_Filename);
 }
 
-void SysConf::UpdateLocation()
+void SysConf::UpdateLocation(const Common::FromWhichRoot root_type)
 {
   // if the old Wii User dir had a sysconf file save any settings that have been changed to it
   if (m_IsValid)
@@ -429,11 +433,8 @@ void SysConf::UpdateLocation()
   // Clear the old filename and set the default filename to the new user path
   // So that it can be generated if the file does not exist in the new location
   m_Filename.clear();
-  // Note: We don't use the dummy Wii root here (if in use) because this is
-  // all tied up with the configuration code.  In the future this should
-  // probably just be synced with the other settings.
-  m_FilenameDefault =
-      File::GetUserPath(D_WIIROOT_IDX) + DIR_SEP WII_SYSCONF_DIR DIR_SEP WII_SYSCONF;
+  // In the future the SYSCONF should probably just be synced with the other settings.
+  m_FilenameDefault = Common::RootUserPath(root_type) + DIR_SEP WII_SYSCONF_DIR DIR_SEP WII_SYSCONF;
   Reload();
 }
 
diff --git a/Source/Core/Common/SysConf.h b/Source/Core/Common/SysConf.h
index 97b3a98232..5eaed702d7 100644
--- a/Source/Core/Common/SysConf.h
+++ b/Source/Core/Common/SysConf.h
@@ -13,6 +13,7 @@
 #include "Common/CommonTypes.h"
 #include "Common/Logging/Log.h"
 #include "Common/MsgHandler.h"
+#include "Common/NandPaths.h"
 
 namespace File
 {
@@ -79,7 +80,7 @@ struct SSysConfEntry
 class SysConf
 {
 public:
-  SysConf();
+  SysConf(Common::FromWhichRoot root_type);
   ~SysConf();
 
   bool IsValid() { return m_IsValid; }
@@ -176,13 +177,13 @@ public:
   bool SaveToFile(const std::string& filename);
   bool LoadFromFile(const std::string& filename);
   bool Reload();
-  // This function is used when the NAND root is changed
-  void UpdateLocation();
+  void UpdateLocation(Common::FromWhichRoot root_type);
 
 private:
   bool LoadFromFileInternal(File::IOFile&& file);
   void GenerateSysConf();
   void Clear();
+  void ApplySettingsFromMovie();
 
   std::string m_Filename;
   std::string m_FilenameDefault;
diff --git a/Source/Core/Core/CMakeLists.txt b/Source/Core/Core/CMakeLists.txt
index a1c72eba39..a5825e15e7 100644
--- a/Source/Core/Core/CMakeLists.txt
+++ b/Source/Core/Core/CMakeLists.txt
@@ -16,6 +16,7 @@ set(SRCS	ActionReplay.cpp
 			NetPlayServer.cpp
 			PatchEngine.cpp
 			State.cpp
+			WiiRoot.cpp
 			Boot/Boot_BS2Emu.cpp
 			Boot/Boot.cpp
 			Boot/Boot_DOL.cpp
diff --git a/Source/Core/Core/ConfigManager.cpp b/Source/Core/Core/ConfigManager.cpp
index eade56d195..a6a8c3e3b1 100644
--- a/Source/Core/Core/ConfigManager.cpp
+++ b/Source/Core/Core/ConfigManager.cpp
@@ -12,6 +12,7 @@
 #include "Common/FileUtil.h"
 #include "Common/Logging/Log.h"
 #include "Common/MsgHandler.h"
+#include "Common/NandPaths.h"
 #include "Common/StringUtil.h"
 #include "Common/SysConf.h"
 
@@ -355,7 +356,7 @@ void SConfig::SaveSysconfSettings(IniFile& ini)
 
 void SConfig::SaveSettingsToSysconf()
 {
-  SysConf sysconf;
+  SysConf sysconf{Common::FromWhichRoot::FROM_CONFIGURED_ROOT};
 
   sysconf.SetData<u8>("IPL.SSV", m_wii_screensaver);
   sysconf.SetData<u8>("IPL.LNG", m_wii_language);
@@ -687,7 +688,7 @@ void SConfig::LoadSysconfSettings(IniFile& ini)
 
 void SConfig::LoadSettingsFromSysconf()
 {
-  SysConf sysconf;
+  SysConf sysconf{Common::FromWhichRoot::FROM_CONFIGURED_ROOT};
 
   m_wii_screensaver = sysconf.GetData<u8>("IPL.SSV");
   m_wii_language = sysconf.GetData<u8>("IPL.LNG");
diff --git a/Source/Core/Core/Core.cpp b/Source/Core/Core/Core.cpp
index 35029c911c..992bc87b6d 100644
--- a/Source/Core/Core/Core.cpp
+++ b/Source/Core/Core/Core.cpp
@@ -24,7 +24,6 @@
 #include "Common/Logging/LogManager.h"
 #include "Common/MathUtil.h"
 #include "Common/MemoryUtil.h"
-#include "Common/NandPaths.h"
 #include "Common/StringUtil.h"
 #include "Common/Thread.h"
 #include "Common/Timer.h"
@@ -65,6 +64,7 @@
 #include "Core/PowerPC/JitInterface.h"
 #include "Core/PowerPC/PowerPC.h"
 #include "Core/State.h"
+#include "Core/WiiRoot.h"
 
 #ifdef USE_GDBSTUB
 #include "Core/PowerPC/GDBStub.h"
@@ -990,7 +990,7 @@ void UpdateWantDeterminism(bool initial)
     // We need to clear the cache because some parts of the JIT depend on want_determinism, e.g. use
     // of FMA.
     JitInterface::ClearCache();
-    Common::InitializeWiiRoot(g_want_determinism);
+    Core::InitializeWiiRoot(g_want_determinism);
 
     Core::PauseAndLock(false, was_unpaused);
   }
diff --git a/Source/Core/Core/Core.vcxproj b/Source/Core/Core/Core.vcxproj
index 599aa36e07..d18d130422 100644
--- a/Source/Core/Core/Core.vcxproj
+++ b/Source/Core/Core/Core.vcxproj
@@ -263,6 +263,7 @@
     <ClCompile Include="PowerPC\PPCTables.cpp" />
     <ClCompile Include="PowerPC\Profiler.cpp" />
     <ClCompile Include="State.cpp" />
+    <ClCompile Include="WiiRoot.cpp" />
   </ItemGroup>
   <ItemGroup>
     <ClInclude Include="ActionReplay.h" />
@@ -464,6 +465,7 @@
     <ClInclude Include="PowerPC\PPCTables.h" />
     <ClInclude Include="PowerPC\Profiler.h" />
     <ClInclude Include="State.h" />
+    <ClInclude Include="WiiRoot.h" />
   </ItemGroup>
   <ItemGroup>
     <Text Include="CMakeLists.txt" />
diff --git a/Source/Core/Core/Core.vcxproj.filters b/Source/Core/Core/Core.vcxproj.filters
index 074218bbe1..4b33dd2e2e 100644
--- a/Source/Core/Core/Core.vcxproj.filters
+++ b/Source/Core/Core/Core.vcxproj.filters
@@ -156,6 +156,7 @@
     <ClCompile Include="NetPlayServer.cpp" />
     <ClCompile Include="PatchEngine.cpp" />
     <ClCompile Include="State.cpp" />
+    <ClCompile Include="WiiRoot.cpp" />
     <ClCompile Include="ActionReplay.cpp">
       <Filter>ActionReplay</Filter>
     </ClCompile>
@@ -794,6 +795,7 @@
     <ClInclude Include="NetPlayServer.h" />
     <ClInclude Include="PatchEngine.h" />
     <ClInclude Include="State.h" />
+    <ClInclude Include="WiiRoot.h" />
     <ClInclude Include="ActionReplay.h">
       <Filter>ActionReplay</Filter>
     </ClInclude>
diff --git a/Source/Core/Core/HW/HW.cpp b/Source/Core/Core/HW/HW.cpp
index efb8590355..732009258b 100644
--- a/Source/Core/Core/HW/HW.cpp
+++ b/Source/Core/Core/HW/HW.cpp
@@ -4,7 +4,6 @@
 
 #include "Common/ChunkFile.h"
 #include "Common/CommonTypes.h"
-#include "Common/NandPaths.h"
 
 #include "Core/ConfigManager.h"
 #include "Core/Core.h"
@@ -24,6 +23,7 @@
 #include "Core/HW/WII_IPC.h"
 #include "Core/IPC_HLE/WII_IPC_HLE.h"
 #include "Core/State.h"
+#include "Core/WiiRoot.h"
 #include "DiscIO/NANDContentLoader.h"
 
 namespace HW
@@ -50,7 +50,7 @@ void Init()
 
   if (SConfig::GetInstance().bWii)
   {
-    Common::InitializeWiiRoot(Core::g_want_determinism);
+    Core::InitializeWiiRoot(Core::g_want_determinism);
     DiscIO::cUIDsys::AccessInstance().UpdateLocation();
     DiscIO::CSharedContent::AccessInstance().UpdateLocation();
     WII_IPCInterface::Init();
@@ -64,7 +64,7 @@ void Shutdown()
   {
     WII_IPC_HLE_Interface::Shutdown();  // Depends on Memory
     WII_IPCInterface::Shutdown();
-    Common::ShutdownWiiRoot();
+    Core::ShutdownWiiRoot();
   }
 
   SystemTimers::Shutdown();
diff --git a/Source/Core/Core/IPC_HLE/WII_IPC_HLE_Device_usb_bt_emu.cpp b/Source/Core/Core/IPC_HLE/WII_IPC_HLE_Device_usb_bt_emu.cpp
index eda94545bc..f81169a140 100644
--- a/Source/Core/Core/IPC_HLE/WII_IPC_HLE_Device_usb_bt_emu.cpp
+++ b/Source/Core/Core/IPC_HLE/WII_IPC_HLE_Device_usb_bt_emu.cpp
@@ -12,6 +12,7 @@
 #include "Common/FileUtil.h"
 #include "Common/Logging/Log.h"
 #include "Common/MsgHandler.h"
+#include "Common/NandPaths.h"
 #include "Common/StringUtil.h"
 #include "Common/SysConf.h"
 #include "Core/Core.h"
@@ -38,17 +39,10 @@ CWII_IPC_HLE_Device_usb_oh1_57e_305_emu::CWII_IPC_HLE_Device_usb_oh1_57e_305_emu
     u32 _DeviceID, const std::string& _rDeviceName)
     : CWII_IPC_HLE_Device_usb_oh1_57e_305_base(_DeviceID, _rDeviceName)
 {
-  SysConf sysconf;
-  if (Core::g_want_determinism)
-  {
-    // See SysConf::UpdateLocation for comment about the Future.
-    sysconf.LoadFromFile(File::GetUserPath(D_SESSION_WIIROOT_IDX) +
-                         DIR_SEP WII_SYSCONF_DIR DIR_SEP WII_SYSCONF);
-  }
-  else
-  {
+  SysConf sysconf{Core::g_want_determinism ? Common::FromWhichRoot::FROM_SESSION_ROOT :
+                                             Common::FromWhichRoot::FROM_CONFIGURED_ROOT};
+  if (!Core::g_want_determinism)
     BackUpBTInfoSection(&sysconf);
-  }
 
   // Activate only first Wii Remote by default
 
diff --git a/Source/Core/Core/WiiRoot.cpp b/Source/Core/Core/WiiRoot.cpp
new file mode 100644
index 0000000000..d0be403339
--- /dev/null
+++ b/Source/Core/Core/WiiRoot.cpp
@@ -0,0 +1,57 @@
+// Copyright 2016 Dolphin Emulator Project
+// Licensed under GPLv2+
+// Refer to the license.txt file included.
+
+#include <string>
+
+#include "Common/CommonPaths.h"
+#include "Common/FileUtil.h"
+#include "Common/Logging/Log.h"
+#include "Common/NandPaths.h"
+#include "Common/SysConf.h"
+#include "Core/WiiRoot.h"
+
+namespace Core
+{
+static std::string s_temp_wii_root;
+
+void InitializeWiiRoot(bool use_temporary)
+{
+  ShutdownWiiRoot();
+  if (use_temporary)
+  {
+    s_temp_wii_root = File::CreateTempDir();
+    if (s_temp_wii_root.empty())
+    {
+      ERROR_LOG(WII_IPC_FILEIO, "Could not create temporary directory");
+      return;
+    }
+    File::CopyDir(File::GetSysDirectory() + WII_USER_DIR, s_temp_wii_root);
+    WARN_LOG(WII_IPC_FILEIO, "Using temporary directory %s for minimal Wii FS",
+             s_temp_wii_root.c_str());
+    static bool s_registered;
+    if (!s_registered)
+    {
+      s_registered = true;
+      atexit(ShutdownWiiRoot);
+    }
+    File::SetUserPath(D_SESSION_WIIROOT_IDX, s_temp_wii_root);
+    // Generate a SYSCONF with default settings for the temporary Wii NAND.
+    SysConf sysconf{Common::FromWhichRoot::FROM_SESSION_ROOT};
+    sysconf.Save();
+  }
+  else
+  {
+    File::SetUserPath(D_SESSION_WIIROOT_IDX, File::GetUserPath(D_WIIROOT_IDX));
+  }
+}
+
+void ShutdownWiiRoot()
+{
+  if (!s_temp_wii_root.empty())
+  {
+    File::DeleteDirRecursively(s_temp_wii_root);
+    s_temp_wii_root.clear();
+  }
+}
+}
diff --git a/Source/Core/Core/WiiRoot.h b/Source/Core/Core/WiiRoot.h
new file mode 100644
index 0000000000..7174fd9943
--- /dev/null
+++ b/Source/Core/Core/WiiRoot.h
@@ -0,0 +1,11 @@
+// Copyright 2016 Dolphin Emulator Project
+// Licensed under GPLv2+
+// Refer to the license.txt file included.
+
+#pragma once
+
+namespace Core
+{
+void InitializeWiiRoot(bool use_temporary);
+void ShutdownWiiRoot();
+}