First : except when there's a need for close-up pictures of threaded objects it is sheer madness to use helical cutouts.It isslowing down every operation, and keeping a nut and a bolt oriented that the threads don't interfere when you move is an exercise in it's own, especially whena number of parts are used in different combinations (I know because I have been there).
Second : it is the way that ProE has taken to handle thread that is making things difficult. Thread is a separate surface, and that makes it behaving bad. Floating in mid-air in exploded views (is that one solved yet ? ) and getting inside solid parts (making it impossible to use it in rendering). The good solution is to make thread an attribute of the hole (or cilinder) only and to make the cilindrical surface inherit this condition.
Alex