I've been encountering a bizzare exporting error with the original FF exporters for 3ds max 5. I don't have images of it on hand, but essentially pieces that I physique, usually to one bone, will end up a short distance away from the actual mesh, and unfortunately any attempts to skope the piece over by manipulating the skin instance do not work. The insane thing is, the pieces will work just fine in 3ds max, and I can't think of any reason for why they are glitching like they are.
I really do not understand it, unfortunately. I'm going to try downloading fresh copies of the exporters and see if that helps, but I don't know if that'll help much. As it stands I can usually just fix everything in nifskope by just moving the appropriate pieces onto the correct bones and deleting the skin instance, but it's alot of unnescessary hasdle and time I could be spending progressing on my other projects.
Check the pieces arent also linked to the bip.
What you describe sounds like both linking and physique-ing at the same time.