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We are doing essentially the same thing here: using Visual Studio 2003 and Perforce. The main thing we do differently is to disable Perforce integration with the IDE.
Neither of the Make VS.Net and Perforce actions do anything unusual that could cause the situation you are describing. It sounds like there is a bug in the software integrating Perforce with the Visual Studio .Net IDE. The problem could either be with Microsoft or Perforce code.
How do you ever get it back into sync once it get's confused?
We've heard of other reasons not to use source control integration with the IDE, this sounds like another one.
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