VS 2008 keeps removing and re-adding <SubType>ASPXCodeBehind</SubType>
For me, the difference depends on whether or not the web project is open in Visual Studio.
I find if I commit the project file to version control with the project open in Visual Studio the SubType elements are present. Closing the solution/project then removes the SubType elements from the project file. Now I always ensure my commits are performed with the project closed in VS to avoid unnecessary changes to the project file.
Working on VS2010 and solved this issue by deleting solutionFileName.sln.DotSettings.user file and solutionFileName.suo. That helped me, give it a try.
Splitting the content of your file into multiple files - one file per class may help.
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