I do not understand the wiring from the description given, but if the batteries are parallel wired and you are measuring different voltages on them, then they are not (effectively) parallel wired - even if one is bad. I also don't understand why they would be independently wired to the panel. Sometimes that was done in boats in the past so you could run on one at a time (using a 1 <-> 2 type battery switch) but that practice has been given up as a bad idea. If the battery shop actually load tested them, my best guess is that there is a wiring problem somewhere.