Problem with stepper motor

I just upgraded my system to the new linux/CommandCNC and am currently trying to configure/debug it. My A axis motor, which runs the far side Y axis stepper won't run, It is selected in the configurator and it is checked for reverse direction. None of the polarity boxes are checked. I pulled the plug out and tested the resistance as in the manual - I get the result shown, about 2 ohms on either side-by-side test of the outer two plugs and infinite resistance on alternate ones (1st and 3rd or 2nd and 4th). I swapped the two plugs that go to the Y axis so the one that moved was plugged into the socket on the bladerunner box for the one that didn't move and vice versa. I still get no movement on the far side of the table. The last thing I tried was checking the stepper windings with an led, Curiously, the motors that work don't light the led, the motor that isn't working does (both windings light when tested). Seems like it must be the motor but not sure what is wrong with it - anybody have an idea?

That explains it. It starts to make sense, that it did not make sense:-).