If your reading really is just 12v and not for example, 12.8 your batteries really are low, about 25% charged, as the helm display shows. 12.6v or above,read when the batteries are not on charge and have not just used, indicates full.
The 5 hours between your last 2 posts is not enough time to recharge them. I don`t know the capacity of the charger, or if it is trying to charge all 4 at once, or how the charge is divided between banks, if they are separate. But before condemning the batteries, give them a good long charge, 24hrs would be good.
As your batteries have opening caps you can remove them to see if the cells are bubbling under charge. Remember the liquid in the batts is sulfuric acid, not water, so be careful doing this, it doesn`t agree with clothing, skin, eyes, etc. If you see that only 2 of 4 cells of a battery are charging, the other 2 are likely dead and so is the battery. You may need to top up during charging, liquid needs to cover the plates or be up to any indicators, forming a meniscus or "fish eye" look.
The hydrometer test readily available and cheap at boat or auto parts shops) is a better test than voltage, but again, only worth doing after the batts are as charged as they can be. An info "how to" sheet should come with the hydrometer.
I suggest resolving battery condition before blaming other items. I don`t think you are there yet. There are way smarter elec guys here who I hope will help.