I think I've faced something similar in the past, and after some digging and trying different things it turned out to be the number of variables / forms / controls that we had in the project. There is a limit to the number of unique variable, constant, and control names you can have in the project.
The way we proved it was to add the module that didn't quite break it, then add an empty module. In the empty module start adding variables until it breaks, it shouldn't take to long.
We cured it by going through the code and changing names of labels on forms to be control arrays, using constants for strings, and removing any code that was old an no longer required. Try to remove unused variables as well.
If it makes life easier you could try moving some of the code out to dll's. Hope this helps.
Cast your eye over this, the sub sections might help: VB6 Project Limitations