catch 1 - 11/14/2015 9:03 AM
Get a volt meter and check the output to each battery with the charger on. Each bank should be fused did you check the fuses? Are both batteries the same size and age?
Pretty much agree with catch1 Everyone must have a meter unless they live in a cardboard box. Each + lead going to T/M should have a fuse. Check both. If both aren't fused, drop back and take care of that first. A 24V T/M will run on 12V's but only about half speed, however the Fortrex controls are designed for 24V's and may/should just sit there waiting on another 12V's before operating, never tried it. I also advise against running on 1/2 voltage unless you have no choice.
Smart Chargers are too smart sometimes and see battery death long before it happens. Check the fuses on charger leads. Not sure what kind you have and how it'll act if one is blown
Swapping batteries around could reveal something but are heavy and a meter should be able to find any issue that swapping batteries would show you
Verify all mechanical connections are clean. Re-make any crimped connection if fuses and batteries all test good. You really can't be 100% sure on a crimped connection, just by looking or wiggling it. I solder/shrink tube everything because marine conditions and crimped connections just don't make sense to my pea brain...unless circumstances require it for temporary fix.
Different length leads on the batteries will draw differently as RR stated but shouldn't cause your issue but it does mess with my mind. I'm sure (I hope) lack of room or boat balance made the bow/stern setup necessary.
Good luck and the more details the better, if you still have issues