Sounds very much like you have a DC load on the batteries which the little charger is struggling to keep up with. Frig, maybe?
Yes, the charger is a bit undersized for the battery
bank you have. A charger in the 50-75A range would be better. In your stead, I'd be tempted to pick up an Iota
DLS-55/IQ4 or DLS-75/IQ4 to handle the battery charging task, keeping the Mastervolt in reserve for when you are dockside and don't have any DC loads of significance. These chargers are relatively inexpensive and do a terrific job....under $200. Check on eBay or on Arizona Wind
and Sun's site (excellent supplier).
Are you hurting your batteries? Probably not in the short-term, but matching the charger to the house battery bank and characteristic DC load would be a good idea.