Battery Charger Test
In addition to testing the charger, check all the connections from the charger to the batteries. Make sure they are all clean, bright, and tight. Include all the grounding wires in your check. I had a similar issue where my charger was charging one bank fine, the other bank was always low. Ended up being a loose connection.
If you have a good digital voltmeter test the voltage at charger output. Then check the voltage at the battery. If they differ, you have resistance in your circuit that will cause undercharging. An analog meter is not sufficiently accurate for this test.
I would also strongly recommend Calder''s "Boatowner''s Mechanical & Electrical Manual: How to Maintain, Repair, and Improve Your Boat''s Essential Systems". That book and a good digital multimeter will enable you to troubleshoot most electrical issues on a boat.