How many motors sometimes these speed controllers are too clever for their own good.
They tend not to like driving 2 drill motors off the same channel had this with Tron with a Sabretooth dual 24A,
Also if there is a small fault on one of the motors it can detect this try each motor connected at a time.
I had this with Kettle bot found one motor all OK the other was U/S even though it worked direct to the battery.