Dead Starter Batteries when Gen Set Running?

Had her out this weekend at the beach and ran AC and DC on with Gen Set running.  Went to start after 5-6 hours and had nothing at 1st then got one to fire on Emergency but not the 2nd.  Waited 10-15 min and then second started. Assume engine 1 charged batteries enough for Battery to fire engine 2?  Shouldn't Gen set charge batteries when its on if switch for Bat Charger is on in control panel?  Any ideas on fix so it doesn't happen again?  Never had a problem when boat is on shore power. Thanks


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