Did you delete the history on the model, after you UV'd it?
If all else fails, just export it using the option box. Just export the model, and only export the uv and model information. Import it back in and do the joint wheight painting again.
I once found out that the uv's on a russian fur hat were going all over the place after I rendered a animation... it used a fur system and it went all over the place... Was a intersting artifact though.