Recently, when I plug my charger in, 2 of the 3 banks switch to "check connection". I changed the fuses hoping it would be something easy like that but no luck. Other than the obvious cleaning the connections, any other ideas what I might try to fix the issue? I thought about getting new fuse holders and seeing if that helped as well. Not sure what the life expectancy is on these things, but I'm assuming it was put on the boat when the boat was new, so it's not even 5 years old. 

Clean all connections good.

Swap each bank one at a time to the battery that does work and try it each time to see if they recognized it.  I have a 330D in one boat and last year, an new battery went belly up and it was doing that.  Two week old group 31 battery, put my Megtronic's tester on it and it was showing 4.3 volts and 23 CA.  Charger was seeing it as an open circuit.  Since that was only the second time those batteries had been charged, I just swapped out that one for a new one and it has been working fine since.