I guess VLC is having some problems running .sub files.
Besides the problems mentioned in the topic named "Subtitles", I just found a .sub subtitle that ran perfectly on VobSub under WMP10, but got out of synch on VLC. Actually, it was never synchronized. :P
If you want to check the files yourselves:
sub file:
ed2k://|file|Charlie%20And%20The%20Chocolate%20Factory%20(DVD-Rip).sub|73562|7B06AB3A3161B94C25C4FEB17F3C049B|h=BVIPALK3JMUHEHPTKZ6MWBIGVM6L27QT|/
movie file:
ed2k://|file|Charlie%20and%20The%20Chocolate%20Factory%20(DVD-rip).avi|743317504|CB6C3DF7817F65F0ED9E23FC4D846376|/