RE: Battery or alternator?
Brabus.
If I were you, I would take ground at the same place as your original battery, or at the very least, at the same place as you grounded your main amps. Did you fuse the secondary circuit? What stops the second battery to suck current through their common plus point?
A parallel connection is preferable, unless listening in a off-engine mode is desireable. A dual battery isolator is needed if you want a separate circuit. A smart one can steer the charging to where it's most needed. And where to take power according to specific or variable parameters. Be careful when operating with a drained secondary battery, it can strain your generator. A capacitator would help, but costs.
I agree with the others as far as the symtoms concurs with a faulty sensor, but it might also be the controller itself, or you might have tampered with ABS wiring somehow when installing the second battery. Maybe you shorted the plus at a vunerable place or circuit?
Using Spanners method will give you an indication of error in the aft sensor, because it has a different resistance value than the front ones. Measuring the resistance is easier. Besides, the one in the back very seldom fails. By reading what you write, I get a feeling of ECU malfunction. Did you get any response out of the DTC reading?
But the very first thing I would do, is take a proper gauge black copper wire and ground the negative pole of the second battery same place as the other.
Regards
Geir