Definitely upgrade to TFS 2008 and Visual Studio 2008, as this is the version of Team Team v2 in every way. Eliminates many small and medium problems.
As for "things that are randomly checked," this is almost always due to the fact that Visual Studio decides to edit files on your behalf. Try to get the latest information from Team Explorer, and nothing is open in Visual Studio, and see if this behavior persists. I bet it won't be!
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