Hi Yakov;
FYI: I spent about a month last year looking at this very type of issue at one of my Canadian government clients (HRSDC) on one of their big human resources applications. Between the HRSDC develop and I we tried various options and could never make the build EXE work from ORCAScript - even with a clean generation. The only way we made the EXE build correctly was from the PB IDE.
I suspect that there are still some bugs in ORCAScript that need to be resolved when compiling large PB applications. I feel your pain on this one (been there, done that).
Regards ... Chris