Maybe you are using VobSub.
BSPlayer displays subtitles by itself.
VobSub does display subtitles too.
This is conflicting with each other.
A better alternative for VobSub is DivxG400.
This one is not active when using BSPlayer,
but does show subtitles when using Media Player.
So this is exactly what you need.
http://www.tac.ee/~prr/videoutils/divxg400.html