It may be a distance thing. I had a spare battery in the bed of my Chevy.
At first I ran 1 alternator and 2 batteries. If I played the stereo hard (about 140-150A on the line side) the second battery would go dead. I had a 170-180A alternator so power supply is not the problem. This battery was killed in about 6 months. I changed to a D-8 dozer battery for the rear hoping the 225+ minutes of reserve would cure the problem. The battery would have the same problem. After 5-6 passes at compatition with the engine running I would have to let the truck sit on a charger to regian full stregnth. I put an ammeter on the line going to my amps. During comp. it would pull 160+A and when sitting and charging with stereo off it would pull 5-6A until charged and then pull <1A.
Got pissed and put a second alternator on and ran a seperate power system for the steroe. Upgraded to 3 D-8 bateries and called it quits. No charging problem.
Now as far as the 1 alt. and 2 batt. problem. I can not figure it out. Could have been differance in batteries. Or the voltage drop across 14 ft. 1/0 power cable. Or the amps just sucked on the rear batt. so much the resistance went high. I'm not sure and I'm an electrical engineer.
When I seen the dual bat. with out an isolator in our cummins I figured they got away with it by using the drive side as a primary and pass. side as a secondary bat. That is why everything (charging and load) is hooked to the driver side. That is why I suggested and going with my experience to use the drive side only. Logic says its all one node, but does it actually act as one node?
Edit- Just for completeness I was Running 3000+ Watts, 4 orion 12's, 14 high end speakers, 2 180 amp alternators, 3 D-8 (dozer) batteries, dual 1/0 runs from second alternator, and 4. 0 farad of caps.