The motor drive is very simple and only runs as powered by the 12volt. The controller simply reverses the polarity to power in and out.
Since you tested the drive and it works, the problem is most probably in the control box.
The only other part is the break (magnet) switch in the door frame...tells the step when to open.
The controller is a sealed unit, and must be replaced as a whole.
We found one on eBay when ours failed in the same manner. eBay had the best price we could find.
Best luck