Hi Greg
I just had a similar problem with my MinnKota 212, 6 amp, 2 bank. After checking all the fuses, I swapped leads from one battery to the other, problem stayed with that particular output. Called MinnKota technical help, They verified what I did and agreed with my suspicion that that particular output was bad. 2 months out of warranty. Too bad, they couldn’t help me.
Just bought a replacement charger, but not a MinnKota.
There really isn’t much to troubleshoot on these chargers, but, I would check the battery lead fuse(s) with an ohm meter to ensure it’s good, not just visually. Then I would power it up, checking the charger output voltage at a set of leads that are working and compare it to the suspect leads. If you’re not getting any voltage output, you’re probably in the same boat as I was.
Good luck
Don