I had the same problem with my 24v system and cranking system. Thought it was my inboard charger (10 amp). Took the batteries to my Interstate distributor. I had one battery go bad and had to replace with a Walmart unit. Found that I did not have a proper cranking battery for a 90 hp Mercury and not the proper batteries for the trolling motor. Well after $350, problem solved. Units are now showing green in the morning. I would us the TM for 2-6 hours and still had 2-3 bars showing on the batteries. By the way, I spent a lot of time looking for a problem in my wiring, connections, on board charge, etc.. All a waste of time. Should have started at the power source first. Would have saved a lot of time.
By the way, this started a the Crescent Lake tournament in January. The second day my batteries when totally dead at 10:30. Had to be towed in when the wind just calmed down. Could have gone to where I new the fish were.
From Steve Wunderele - 10-2-84 --"A fishing trip maybe brief, but it's memories are endless."