Trolling Motor Help

I recently bought a boat with minn kota terrova trolling motor and first few trips everything was working fine. This weekend I went to use my trolling motor and it was barely moving the boat on the lower speed settings and would go into a clunky, slow spin when I went above 5 on the dial. The batteries are showing full on the charger and on the built in tester on the trolling motor. The i pilot remote shows "motor lost" when I tried to turn the speed up.

The boat also has a cd player that the previous owner wired up with alligator clips so that he could plug it into the trolling motor batteries whenever he wanted it on. I left them plugged up to the battery on accident when I left July 4th weekend and I am also not getting power to the radio. I checked fuses and they were ok.

Possibly a bad battery...

Check all the connections going from the battery to the trollingmotor, especially at the battery. A bad connection will operate a simple battery tester but will not carry the load of a trollingmotor.
John

Turns out there was blown fuse on the radio after all and the battery it was hooked up to was dead (1 of the 2 trolling motor batteries) . I noticed during this process that the three bank charger only shows 2 banks charging even though there is wires going to each battery. Is this normal?

No. If you have 3 batts and 3 batts are attached to the charger, when plugged in you should at least get a green light if the battery is charged. If 1 bank is not lighting up in any way, it is time to buy a new charger.

A dead battery may not have enough in it to allow the charger to read it. Before ditching the charger, replace the battery and see if the lights come on.

Ok sorry new boat and i'm still figuring the nuances out. The charger is a bass pro xps and the two lights being on are actually an indicator that something isn't right with them, but the charger will show the full charge.