Quick idiot check before anyone else asks you have got mk2 software on it also does the fader work from from to rear.

What i tend to do is using balance and fader sweep round each corner of the car to check everything is okay

but i think what you are saying is it don't want to let you stay in four channel mode on the fader, If this is your first time out with 2.0 it is different in the way the equaliser works from 1.0

Can't remeber exactly how to save setting in 2.0 without empeg in front of me but it is different but check the fader first as it is going to shed a bit more light on your problem, also if you can be arsed and you have the original head unit stick that in and see if it drives the rears okay