HI BruceT
It's nice to know that someone else is having similar problems, I was beginning to think that I was the only one who used the 3D hole (and nut and bolt) stuff. Yes you're right, it is a really pain. It makes no difference even if you're using a different working plane, everything gets aligned to the ground plane and not even position to the insertion point.
It seems to apply to bolts, holes and most 3D plug-in objects in the Machine design module.
Can I ask, do you have any problems with the 3D holes (or bolts) realigning themselves after saving and then re-opening a file? That is also a pain and never happened with VW 2008. I have been on to NNA but they don't seem to be able to replicate this anomaly.
All the best
Guy