First time CNC builder cloned Y axis issue

I have just built a cnc and I am doing the initial configuration, setup and testing. I’m using arduino uno and Cnc shield 3. Most things are going fine but I have two outstanding issues. The first one is that my cloned Y axis is cloning steps correctly but not direction. In other words the cloned A axis only moves on one direction. So if I jog in the Y+ direction both sides of the gantry (Y and A) move together as expected. However when I jog in the Y- direction one side returns but the other side keeps moving further in the original + direction causing the gantry to skew.. The jumpers are wired correctly. Any thoughts on what might be happening?

UPDATE: this cloning issue is now resolved it was in retrospect the most obvious problem .. a faulty (homemade) jumper

The second issue is that the z axis limit switches are not being detected by the Universal Gcode sender. (X and Y are fine)..

Any help is much appreciated.

Could You post links to, or photos of, the driver board? Is it a red Prootooner board?
Some schematics would be good as a reference for further dialogues.

Post a photo showing the jumper positions.

This shows the correct jumpers for cloning the Y axis.

Did you enable variable spindle speed control (or laser control)? If so, from this page:

For Grbl v0.9 and v1.1+ default builds: (NOTE: Z-limit is on D12 and the spindle enable pin uses the hardware PWM on D11.)

UGS may be expecting the Z limit on pin 11 instead of 12. Z limit was on pin 11, by default, on older versions of grbl. I don't know how to fix that in UGS.

Great thank you.

I don’t require variable speed control but it may it still be enabled. If so I would like to disable it and use z limit switch.

You were right re my false assumption the jumpers were wired correctly. They looked like they were but one was faulty.

In the config.h file at around line 339 comment the line "#define VARIABLE_SPINDLE" to disable the variable spindle speed.

Where are those jumper wires on the clone headers going? To clone an axis you just need to jumper (short) the pins as shown on the image that I posted before. You don't connect them to anything off the shield.

Thanks. Will investigate the z axis limit switch issue.

The Y axis cloning is has been resolved by replacing faulty jumper.

Resolved this z limit issue too .. used remapped pin.

Thanks for assistance.

Glad you got it working.