What version of AC3 filter are you using?
Is it
AC3Filter v0.70b or "release candidate"
AC3Filter v1.01a RC5?
(First one only covers AC3 sound; the "release candidate" apparently also covers mp3 sound but I don't use it myself so I've no experience with it.)
Further: what settings are you referring to?
What is selected at "For AC3 decoding use" under rightclick > Options > Preferences > Audio; if not "System default", could you try that?