The Green LEDs you mention are simply connected to one of the motor windings.
They flicker, mostly for entertainment. If the motor stops rotating with a particular winding in a reverse polarity state, the LED will be extinguished, but motor still energized. Summary – flicker is normal.
I see you are already trying $4mi=1, I was going to suggest that.
What command are you issuing to get the motor to move?
e.g. G0 A3000, expecting about 10 stepper revolutions?
If I assume that A rotated normally when disconnected , it does sound like the stepper does not have enough torque to overcome the load presented by the mechanism.