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Voltage regulator seems to be the culprit, and any time a battery is getting hot you have a VERY serious problem because they can pop a cap and release hydrogen gas and it is very explosive. On your system I am wondering if your voltage regulator system is charging both batteries at the same time or whether you have a "battery combiner" that isolates one from another. Otherwise if one battery is down the system will think it needs to charge more, etc.
I hope you can figure it out because a hot battery is a seriuos issue. A 20' Grand Prix is an awesome boat. I agree about having a double battery bank too, basically on any boat. Good luck, send us some photos !