"Correct" IPS applier to resize file if it tries to write off end. I'm not sure what the spec behavior is, but this works for at least one file in the wild.

BizHawk.Client.Common/IPS.cs

@@ -5,7 +5,7 @@ namespace BizHawk.Client.Common
 {
 	public static class IPS
 	{
-		public static void Patch(byte[] rom, Stream patch)
+		public static byte[] Patch(byte[] rom, Stream patch)
 		{
 			var ipsHeader = new byte[5];
 			patch.Read(ipsHeader, 0, 5);
@@ -16,32 +16,40 @@ namespace BizHawk.Client.Common
 				if (ipsHeader[i] != header[i])
 				{
 					Console.WriteLine("Patch file specified is invalid.");
-					return;
+					return null;
 				}
 			}
 
 			// header verified, loop over patch entries
 			uint EOF = ('E' * 0x10000 + 'O' * 0x100 + 'F');
 
+			var ret = new MemoryStream(rom.Length);
+			ret.Write(rom, 0, rom.Length);
+
 			while (true)
 			{
 				uint offset = Read24(patch);
-				if (offset == EOF) return;
+				if (offset == EOF)
+					return ret.ToArray();
 				ushort size = Read16(patch);
 
+				ret.Seek(offset, SeekOrigin.Begin);
+
 				if (size != 0) // non-RLE patch
 				{
 					var patchData = new byte[size];
 					patch.Read(patchData, 0, size);
-					for (int i = 0; i < size; i++)
+
-						rom[offset++] = patchData[i];
+					ret.Write(patchData, 0, patchData.Length);
 				}
 				else // RLE patch
 				{
 					size = Read16(patch);
 					byte value = (byte)patch.ReadByte();
 					for (int i = 0; i < size; i++)
-						rom[offset++] = value;
+					{
+						ret.WriteByte(value);
+					}
 				}
 			}
 		}

BizHawk.Client.Common/RomGame.cs

@@ -90,7 +90,7 @@ namespace BizHawk.Client.Common
 					patchFile.BindFirstOf("IPS");
 					if (patchFile.IsBound)
 					{
-						IPS.Patch(RomData, patchFile.GetStream());
+						RomData = IPS.Patch(RomData, patchFile.GetStream());
 					}
 				}
 			}