I have HAD exactly the same problem.
I do use NOW DivXG400 instead of VobSub.
Now my problem is solved. :D
I see subtitles in Windows Media Player,
which are automatically displayed by DivXG400,
when using same name for movie and subtitle.
When using BSPlayer, DivXG400 does nothing at all,
and therefore it does not conflict each other.
So uninstall VobSub and install DivXG400:
http://www.tac.ee/~prr/videoutils/divxg400.html
:D