when the batteries are hooked up in parallel, you shouldnt be getting the batteries to be reading differently because essentially they are acting like one big 12v battery.
the other thing is unless you are sure the big fuse that is on the ground side is good, you should measure to frame ground.
if you have your charger on and the merge switch on, you will be getting voltage from the inverter/charger as well, so make sure that is not on.
i always isolate the battery to be sure nothing else is effecting it.
what usually happens is that the battery will still be close to 13v but will draw down very quickly under load and that is why it shows up only under a load.
if indeed you are getting a different voltage measuring directly across each battery, it makes me wonder if the cable connecting the two batteries is good or the connections not good.
i would take them off and clean them, and check the battery voltage with the cables off.
my two cents worth.
tom
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