The Make VS.NET action in VBP actually invokes the VS.NET command-line compiler to perform builds, and it's very possible there is a bug in there related to this (although we haven't run into it ourselves yet). If you check the 'show command-line' checkbox on the Options tab of the Make VS.NET action and build, you could use that info to reproduce the problem outside VBP and open a support incident with MS. A list of known hotfixes for VS.NET 2003 is available here:
http://search.microsoft.com/search/r...3+hotfix&na=54