Me and my girlfriend play this and I've unlocked a bunch of stuff.  When she signs in under her own Xbox (off line) profile and goes into the game all of the things I've unlocked are unlocked.  Is there anyway she can have her own separate save game of DJ Hero and unlock only the stuff in her game?

You should double check that you both arn't signed in. I could be wrong but most games treat when you are on separate 360 profiles as almost different consoles.

Maybe your both signed in because the save file should only stick with the profile that was signed in at the time.