Every problem seems weird till you know the reason, so try this one for size.

In stepconfig, I've set the limit switch pins(11,12,13) to "Unused", on the assumption that this will remove any self-inflicted errors, due to my still not being sure what settings to use.
Other pins are set using my controller cct diagram, or set to Unused.
The parameters set on the next pages of stepconfig for X and Y axis are identical, apart from the maximum travel.
Likewise, Z differs only in travel and mm/rev.

Testing X and Z axis, both jog and run work correctly.
Testing Y axis, when I open the "Test this axis" window, I can hear the power go to the motor, and the shaft "locks up".
However, neither Jog nor Run work, unless I open the NC limit switch on that axis, then each works.
I've switched cables, and tested the X motor in the Y socket, and the Y motor in the X socket.
The symptoms show the problem is only associated with the Y socket.
If I have the "Run" on , and ease the plug gently into the Y socket, I can make the Y axis run OK, so some pin when unconnected allows it to work. Pushing right in locks up the Y motor.

I've tried reversing the step and direction settings for the Y axis, and inverting the signal for one or both, but no improvement.

Do these facts point to a specific source of the problem ?
I suspect the controller, but I can't think what would produce this symptom - the supposedly disabled limit switch preventing the step signal getting through, unless the NC limit switch is opened (which ought to have the opposite effect).

John