Matt, are you getting the bass rubbing on radio, CD, or MP3 CD? Do. for the tweeter.
Try giving the tweeter triangle a bash in case it's not sitting right.
Next question, what settings do you have treble and bass at? I have treble at 2 and bass at 4. 4 is a bit much for bass if I have a loud source (MP3 tracks vary in their sound level I find). I have it at 4 because I don't usually play it that loudly but if I play a loud track at high volume, 4 is too much for the subs.