Since the skeletons are being exported uniquely, I'm not sure where the problem is. The only time I have had that kind of problem in the past is under the conditions I mentioned before.
I'd also double-check that the CFG files are all pointing the the appropriate skeletons, and would also see if you get the same problem when exporting them from another computer if you haven't already.
If you want, you can send us a zip archive with some of the problem files to take a look at.
http://www.worldviz.com/support/upload.html