[Jon Stratis]

I'm going to spell out what I think your setup and observations are, then give you the problem and solution, assuming my understanding of the setup and observations are correct.

Setup: You have two motors going into a single gearbox to power each side of the robot. This would be for a normal "tank" drive robot, for example having 6 wheels on each side all chained together.

Observations:
- One side does not move when the code tells it to
- When calibrating the motor controllers, you see:
1. Calibrating controller "1" makes the wheels spin forward when you want them to go forward in the calibration
2. Calibrating controller "2" makes the wheels spin backwards when you want them to go forward in the calibration - ie it acts opposite of controller "1"

Is all of that correct? If so, then I've got another test for you. Unplug controller "2" and try driving. Does that side work as expected? Now, plug that controller back in and unplug controller "1" and try driving. Does that side work as expected?

I suspect you somehow got the motor leads "swapped" for controller "2". As a result, when you try driving forward on that side, motor "1" sees a +12V signal, while motor 2, with the leads swapped, seeings a -12V signal. The motors run against each other and stall in the gearbox. Unplug the motor leads from controller "2", swap them, and plug them back in.