Motorguide/Battery question

[txbasshound]

I have an 82 lb Motorguide on my Bass boat which is a 1998 Astro. The trolling motor will not run when switched to 12v, only runs on 24v. Trolling motor does pretty well but will start to die out after heavy use. My question is, after the trolling motor starts to die out, a check of the batteries will show 1 battery at 4-6 volts and 1 battery still fully charged. Why is it only draining 1 battery and why does it not run at all on 12v?