So,the last time we recorded (With a 12channel mixer,into a pc with a Julio (smth) soundcard) we had this problem.We were recording bass.We imported the Drum track (Audition) for playback,and pressed R on the empty track for bass and started recording,but the drum track also recorded over the bass.What the hell?
so you are recording the playback/output of soundcard.

Are you using a true audio interface or just a stock sound card?
You may have to set your sequencer program to take audio from the input only. This will be in the preferences menu.