Try tapping on the end of the motor litely while you have those wires connected.
It could be a spot on the armature, where the brushes stop every time & bad enough it cant start the motor turning again.
If you think about how that motor works, steps come on & push the steps out & motor stops just about at the same spot every time. Then the steps go in & the motor stops just about the same spot every time, so over time that motor stopping in the same place & under load until the control box turns the 12V off it could cause a spot on the armature & the brushes not make good contact.
Now if a gear in the gear box broke or the gear box housing itself broke, it could cause everything to bind up & that little motor couldnt over come the binding.
You may can unplug the motor wires & then prize on the steps enough to remove some tention on the steps & then can remove that little pin in the gear box arm to release the steps.
Neil