You have a pair of batteries that are reacting differently to how your system is wired.
Thing about balanced or not is its not something you really 'see'.
You will see more available power, with the second battery (or pair of 6s) simply tied in. Yes they will feed each other trying to equalize but this isnt 'balanced'. It will work but optimum isnt something generally seen short term.
I didnt see where you mentioned what generator you have. I am puzzled when you say you have the converter charging one pair, the generator the other pair? Your generator is directly putting out 12v? Most the gen sends 110 to the converter-it sends charge voltage. So charge is from the same source to the same pair of batteries.
Ive probably been out in the sun too long, but what I have read is
Your have 2 pair of batteries 6+6(1 12v ) and 6+6 (1 12v)
they are tied together.
But 1 pair sees direct charge, the other pair only sees what drifts over...
And that pair sees, what Im deducing, the largest load, starting the generator.
Obviously your system works, your getting 4-5 days, My opinion is you are see the long term affect of imbalance. One pair is doing all the work, the other along for ride.
For longevity I would be swapping pairs, though might be a bit late. Seems adding some wire would be easier.
