I do not believe any controller can properly charge two independent batteries from one pos/neg cable. The controller needs to sense battery voltage to know "how" to charge the battery - if there are two batteries connected (not a bank), the controller will not be getting accurate information. Are you sure you do not have two 12V batteries wired together in parallel to create one 12V battery bank? (a charge controller CAN charge a bank of batteries).
The existing set-up is as follows:
A hot and ground come from each panel.
The two hots are twisted together with a pigtail hot going to the controller. There is a 20 amp fuse before the controller.
Two grounds go to the controller.
One hot and one ground come from the controller; Another 20 amp fuse.
The one hot and one ground are split with a hot and ground going to one battery and a hot and ground going to the other battery.
Each battery has a hot and ground coming from, I'm assuming, the inverter; I can't get a good view of the connections without taking out the inverter.
I have appx 6 feet of 14 AWG from the panels to the battery.
The set-up looks like it was done by the manufacturer. I'm guessing parallel battery connections?
My plan is to disconnect the one hot and ground from the second, non-functional panel; I will disconnect before the controller. Anyway, the new panel is coming in a couple of days, fingers crossed.:) Thanks for the advice/considerations