I think that my explanation is enough for the case of developers trying to build GlueGen because some antivirus really believe any program that creates a DLL is a virus except some "known" compilers. However, it does not explain why some people who don't build GlueGen have the same problem. In this case, I think that another viral agent target our DLLs. None of my Windows "users" reproduced this problem.
Yes, I suspect these tools make bad predictions at runtime, based on the behaviour of a program.