I am going to explain way IMHO (not IMHO, but fact. Sorry I can not scientifically explain, so I will use IMHO and you make your own decision,) paralleling batteries is riddled with complications and prone to early battery failure. Charging such a battery system is also a challenge.
I am going to use this reference to back up my info... http://www.nyc-arecs.org/batt1.pdf
Battery School | Batteriesnorthwest.com | Advantages and Disadvantages of using two 12 volt batteries connected in parallel or two 6 volt batteries connected in series.
What these guides do tell you, but do not spell out for you, I will do. First all battery cables have resistance. The longer the cable the more resistance. Just A Little Corrosion Causes Big Voltage Drops as well, acerbating the issue. So any battery that has a cable that is longer or corroded will have more resistance than a battery with cables in better condition. That means that the battery or bank of batteries with bad or longer cables will draw less amps, this giving an uneven draw from each bank.
Now assuming both your battery banks at perfectly identical, and cables are not an issue, almost impossible to have both with the exact state of charge and condition...all the time. The bank or battery with the lower voltage will be the governing output voltage. If one bank is 12.5 V and the other is 12.3 V the voltage of the two in parallel combined will be 12.3 V. Is is an issue with charging system.
And that brings us to your issue. IMHO, in order to charge this system correctly will be to isolate each bank and charge separately. If you are trying to charge both banks with one charging source...Now I am not up on the new chargers and know nothing of the new technology. But on my boat the charger charges until the voltage is reaches a preset point. If the battery system is reading 12.3 V combined, even if one bank if full, the charger will continue to charge both banks, cooking the bank that has a full charge and may never bring the lacking bank up to full charge. That is the extreme, most likely the bank will come up to snuff and charger will shut off, but at the cost of damaging by over charging. Over charging side effect is the boiling off of the water. Also when over charge a battery bank you heat that bank causing increased corrosion of the plates and reduces battery life making the two banks even more out of sink.
I inherited a five, 12v parallel battery system, and could never get it right. The added hydrogen produced from the over charging causes all kinds of issues with corrosion and hardening of rubber and shortening of battery life. And is an explosive gas! Since I went with two 6V 375AH in series, I have had no issues...period! Series is simple, Parallel is riddled with issues unless you have a perfect setup. And there is no such thing as perfect. You might start out with as close to perfect as you can, but this will change with use.