diff --git a/Source/Core/Core/ConfigLoaders/BaseConfigLoader.cpp b/Source/Core/Core/ConfigLoaders/BaseConfigLoader.cpp
index f317bc8324..5cfd42e7bc 100644
--- a/Source/Core/Core/ConfigLoaders/BaseConfigLoader.cpp
+++ b/Source/Core/Core/ConfigLoaders/BaseConfigLoader.cpp
@@ -20,6 +20,7 @@
 
 #include "Core/Config/SYSCONFSettings.h"
 #include "Core/ConfigLoaders/IsSettingSaveable.h"
+#include "Core/ConfigManager.h"
 #include "Core/Core.h"
 #include "Core/IOS/IOS.h"
 #include "Core/IOS/USB/Bluetooth/BTBase.h"
@@ -49,6 +50,9 @@ void SaveToSYSCONF(Config::LayerType layer)
         setting.config_info);
   }
 
+  if (SConfig::GetInstance().bEnableCustomRTC)
+    sysconf.SetData<u32>("IPL.CB", SysConf::Entry::Type::Long, 0);
+
   // Disable WiiConnect24's standby mode. If it is enabled, it prevents us from receiving
   // shutdown commands in the State Transition Manager (STM).
   // TODO: remove this if and once Dolphin supports WC24 standby mode.
@@ -177,4 +181,4 @@ std::unique_ptr<Config::ConfigLayerLoader> GenerateBaseConfigLoader()
 {
   return std::make_unique<BaseConfigLayerLoader>();
 }
-}
+}  // namespace ConfigLoaders
diff --git a/Source/Core/Core/HW/EXI/EXI_DeviceIPL.cpp b/Source/Core/Core/HW/EXI/EXI_DeviceIPL.cpp
index cda6a3eccb..08af03a6da 100644
--- a/Source/Core/Core/HW/EXI/EXI_DeviceIPL.cpp
+++ b/Source/Core/Core/HW/EXI/EXI_DeviceIPL.cpp
@@ -129,6 +129,8 @@ CEXIIPL::CEXIIPL() : m_uPosition(0), m_uAddress(0), m_uRWOffset(0), m_FontsLoade
   // We Overwrite language selection here since it's possible on the GC to change the language as
   // you please
   g_SRAM.lang = SConfig::GetInstance().SelectedLanguage;
+  if (SConfig::GetInstance().bEnableCustomRTC)
+    g_SRAM.counter_bias = 0;
   FixSRAMChecksums();
 
   Common::WriteProtectMemory(m_pIPL, ROM_SIZE);