Alternator

I am just wanting a general consisic of the group on this question. I have a 96 Ford Explorer I have 2 batteries one in the front the other in the rear. I have a isolator which when the truck turns on it supposed to charge the back battery as well as the front. Well the back bettery continue's to die after like 2 or 3 weeks. Do you guys think that it's the Alternator causing this problem, being that it's not strong enough to charge 2 batteries or do you think it could be something else. Thanks for the reply back. The alternator is a stock 90 I believe I am running a mids and high system and a compressor for air bags on the batteries.