I don't have an ACA but here's a quick thread I googled up - see @fitzsteve's post about halfway down for a good summary of ACATune commands:
http://www.amiga.org/forums/archive/index.php/t-68501.htmlMaybe post what settings you're using now (you do have it running correctly as the first line in your startup-sequence, right?), and someone else who owns the accelerator will be able to point out what's wrong?

There's another thread about configuring these that I believe was about 100 posts long, but danged if I can find a link right now!