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My first step would be to look at the connections of your batteries in series, as it appears that there may be a drain on Batt1 that is not on Batt2 or vice versa. There should be ONLY ONE connection from the - side of each Batt1 to the + side of each Batt2, and that should be the heavy cable which combines them in series. ANY other wires will cause the problems you describe. It is not clear whether the Batt2 were discharged more and never recharged, or whether Batt1 was discharged more which resulted in overcharging the Batt2, but the second is more likely if you have gel batteries. Remember that gel batteries can sit around discharged for months without problems, but can be ruined overnight by overcharging, while the opposite is true of wet cell batteries.
Once one battery in a series goes bad, you must replace both batteries with the same type, capacity, and age. They really don't make gel starter batteries, so your captain may have put in a non-gel battery. The drain problem I described above would have killed the replacement batteries anyway.
The latest Mass 24/100 does have a dipswitch setting for gels, which just increases the float voltage.
The 12v system should be isolated by the DC-DC converter, but you can test for unexpected current drain
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