We just managed to isolate the issue. Whenever there is a Y cable plugged in to the cortex, none of the motors run. As it turns out, we Y’d the port off to two motor controllers instead of Y’ing the motor controller off to the two motors.
If I understand what you’re saying correctly, that is exactly what your supposed to do: Y one port to two MC29s to two motors.
From your description, it sounds like you might have a loose connection with the main battery and the cortex is running off the backup battery, but then again I don’t think all the lights should be green. Do you have a backup battery, and if so have you tried unplugging it?
EDIT: Disregard that, just saw your update post. Good to hear it was only a malfunctioning wire.
Not a good idea unless you know what you are doing.
Plugging a two wire motor to center (red) and outside (black) connections would send battery power to the motor which is OK for a test, however, plugging to center (red) and inside (white) connections may damage the cortex. Specifically there is a chance it will damage the ESD protection diodes as described in this thread (that Kevin conveniently linked to earlier today).