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| Chris-Hi- You don't say if you're using a 12V/24V trolling motor- Does your trolling motor batteries have only three cables to the trolling motor? If that's the case the batteries usually aren't discharged equally. As you switch between 12V & 24V operation. The 12V battery- usually the one w/ black wire on the negative post- will be discharged deeper because it's used for both voltages.
Are the two batteries identical- manufacturer,age,AH rating, etc? You also don't say you're not getting the performance you expect, so I'd suspect the above is true- one battery is being discharged more than the other.
"It's your choice to Catch'em & Let'em Go!"
Al
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