Doesn't matter, yes there is some voltage drop to the rear, but 12.4 means it's not being charged like it should. It should be 13.9 minimum, anywhere in the car. You obviously are putting way to much of a load on your alternator and it won't be lasting long. The dual batteries are not helping any. Just because it works, doesn't make it RIGHT!!! however, in this case it's just barely working.
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13.9 anywhere in the car huh? you got your facts messed up man. 13.9 should be at main battery. Wire can drop your voltage by alot then there are accessories along the way and amps in the back. It'll never be 13.9 at the trunk. Your talking voltage here and not current. As long as your not having problems and your lights aren't blinking its fine. And it must be a good alt then cause almost 2 years now and its still running strong. :P Not trying to argue with you man what i have works and its fine and will last.
Any way vtoney you say your voltage drops but its fine at your battery? Where are you checking the voltage when it drops? And whas your system playing while you were checking the voltage at the battery?
I will still emphasis that you upgrade your ground wires and your alternator wires they help alot.