Battery Issue - Need Help!

Guys I am totally at a loss with this problem. About a month ago my trolling motor would not work and I thought it was the mother board. Took it to a dealer and they checked it out. The problem was that one of the batteries had reversed polarity. The interstate battery store said they had only seen this a couple of times and that the battery had to be completely discharged and then hooked up backwards and recharged to reverse the polarity. I told them it could not happen. I have an on board charger so do not hook up the battery. They drained the battery and recharged it for me. Has been ok for the past month. Went a few times and hooked up my on board charger to charge back up. Went Friday and the same problem with the other battery. (24 volt trolling motor) What is going on. Could it be the charger. I completely unhooked it, but hate to spend $200 if that is not the problem. Any ideas?

Attachment 389744 are your batterys connected in series properly? If all your connections are good and proper then maybe something is wrong with your onboard charger.

I have checked and rechecked the connections and how they are wired. All of that is good.

Yep. I agree unless you was monkeying around with the wires and accidentally swapped polarity then it is the charger. I have made that mistake with a blue top crank before.

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I think I will leave the charger unhooked and see if it happens again. Only other thing I could think of is a wire worn somewhere and grounds out at times, but the 2nd battery doing it this time almost eliminates that.