13.7 volt charge rate from the Alternator after 5 hours of running the engine may be all you will get if the house bank started at 12.2V. 12.2Volts is about 50% discharge. I don't know how big the battery house bank is but assuming it is two 105AH batteries in parallel would mean both batteries need 55 AH to be recharged, the engine battery needs charged and is using some power to operate the engine and the thruster battery is being charged probably being a minimal amount but it is in the circuit. When the Engine battery reaches 13 volts for 3 minutes or 13.5 Volts for 30 seconds and the house and thruster banks are above 11 volts the ACR (Auto Charge relays close and all the batteries are charged as one battery. The batteries are not charged individually. While you are running, the boat's 12 volt circuits are using amperage, refrigerator, all the electronics, fresh water pump, fans (if being used), lights, inverter is on, all of theses components are using 12V amperage. Probably not more than 10AH average. If you start with two batteries being at 12.2 Volts the 110 amp alternator which is not putting out 110 amps in that engine compartment. Heat reduces the alternator output, engine speed controls the alternator output. As the engine rpm increases the alternators output increases. The alternators max output is based on 6000 rpm. The pulleys are normally 1 to 2 ratio. Meaning 1 rev of motor the alternator turns 2 revs. If you are cruising at 1500 rpm the alternator is 3000 rpm at this speed you will not be getting full output from the alternator plus you will have a reduction in output because the alternator is most likely operating at 190F + which will reduce its output capabilities because of resistance add the resistance of four batteries being charged.
If the batteries have never been discharged below 50% and always charged to 100% right after the batteries where discharged to 50% it would take 3 to 4 hours to fully charge the batteries in the boat using the alternator. If the batteries have been discharged lower than 50% it would be longer.
From my experiences while long term cruising and staying on the hook at night using three batteries in the house bank. The house battery bank would go below 50%. We would be laying over for an extra day, still using the 12V components and I would have to start the generator to charge the battery banks. Using a 30 amp charger to charge 4 batteries to a full charge 3 of which are at 40% to 50% so the 150 AH needed to recharge using a 30 amp charger would take around 6 hours if you turned all the battery switches off. It would probably take 7 to 8 hours with minimal 12V usage. Running the generator for an hour or two to bump the voltage up does nothing but buy you more time but the fact that you did not fully charge the batteries will start to damage them.
My guess is that is what is going on with your 2 year old batteries. Assuming the batteries are the factory AGM universal that require a full charge after a discharge. If lead acid batteries get a discharge of 50% or lower and do not get a full charge after the batteries begin to loose their capacity. There are folks that get 6 years out of universal AGM batteries and some that get 2 years out of them. I purchased Northstar batteries which are expensive USA manufactured with a high rating and after 2 years I started to see a loss in capacity. Why ? Because I discharged them to 50% or more a several times and did not recharge to 100% because we were anchored out and it would have taken all day using the on board charger and I didn't want to run the generator all day.
I know this is a bit to read to get to the point that Mike is making. Load test your batteries. I would suspect you have at least one battery maybe both in the house bank that is not reaching its capacity and will not fully charge.
