Hi Matthew,
I'd try launching the VSS compare in a different way (from checkin window,
from context menus in solution explorer, from main menu under
File/SourceControl, etc, and see if it changes anything.
We had no reports of such problem with the Diff window in VSS2005, so I have
no idea whether switching to a different viewer will solve the problem.
If you want to try using 3rd party compare aplications, custom viewers can
be configured in VSS Explorer 2005 in Tools/Options/CustomEditors tab

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Alin Constantin
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> We have recently started using Visual Studio 2005 with Visual SourceSafe
> 2005. I have noticed that when doing a compare of my local copy of a file
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> third-party compare application, would this solve the problem? Where in
> the IDE's options do I tell it to use a different compare application?