What voltage batteries are they? If they are 8 volt, they should be reading around 35V for the bank, but then how do you get 24V for the thruster, genny, etc? Do you always run the genny when underway? Are you running an inverter underway? At 41 volts, it's almost impossible for this to be a battery problem, but we need more info.
The first thing I'd do is to turn off the charger at the dock and get voltage readings. That will be your battery bank voltage reading with no charging system running. If fully charged, it should read around 36V for both banks. Take a separate reading at the batteries with a simple digital voltage meter. Make sure that the meters agree so you know that it's not a voltage meter problem.
Next, start up only the port engine and read the voltages. It should still be unchanged at around 35V for the SB side and around 35 to 38 on the port side depending on the alternator. If the voltage jumped up to 41V on the SB side when you started the port engine, there's something strange in your wiring, because normally the port engine won't affect the SB batt bank.
Next, start up the SB engine and read the voltages. If the SB reading jumped to 41V, the problem is your SB engine's alternator is putting out 41V charging current. The battery bank may be just fine, but the alternator is giving you the high voltage. Check you alternator specifications to see what the max charging voltage should be.
If it still reads OK and you normally run the genny when cruising, start the genny and check again. If it jumps up now, it's the charger running off the genny or the combination of the charger and engine alternator.
None of the above problems are the batteries. Let us know what you find and maybe we can help.
Good luck,
Doug Shuman