Are you on iOS 4? Apple acknowledged an issue with iOS 4 and the most current version of GarageBand in which upgrading to iOS 5 resolved.
If you are on iOS 5, restart the iPad and connect your headphones before connecting JAM. If you still have problems, you should get in touch with Apogee support. I have a few products of theirs and they've always been awesome with helping me.
Hope this helps!