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So based on your explanation if I start the boat and the start battery is at 12.8v, the battery has to get to 13.7v before the house battery starts to charge.It can take quite a bit of run time at planing speeds before the stators can recharge the battery. If you have a DVSR, then the start battery has to reach 13.7 volts before it will combine and begin to recharge the house battery. If you are only making 15-30 minute runs between starts, I would not be surprised if the start battery has not recharged enough to activate the DVSR. Most models have an LED on it to show when it is active.
I would start by checking both batteries to rule them out. Also, you can close the emergency parallel switch to let both batteries charge while underway. Just be warned, before they start to charge, they will level out. The higher voltage battery will "send" voltage to the lower until they are both the same. If your house battery is bad, all you did here was lower your start battery. The little charge that you would gain across both batteries would not make this worthwhile in a short run.