Yes, that should work. Attached is a modified version of the VStudio.bld sample that does this (setting the VB projects to no compatibility before building), and it works as expected here when saved in the VisBuildPro\Samples folder and built.
If you can tweak the sample to reproduce the behavior you're seeing, or provide a reproducible case, ZIP it with folders preserved, post it here we can take a look at it. Also see this FAQ for some general recommendations on handling VB builds:
http://www.kinook.com/Forum/showthread.php?threadid=57