This one has me puzzled, maybe someone can help?

I am setting up a new laser engraver, using GRBL, Arduino UNO and CNC shield. The shield has a double Y using cloned A driver.

I had all the setting done correctly I thought, I could move the machine in all the correct directions and then I came to doing the homing.
I pressed the homing button and all moved in the right directions, Z was OK, Y gave a problem (not worked that one out yet) and X didn't complete due to Y having the problem. I will check out all the wiring and connections tomorrow when I have more time as it is late here now.
The strange problem is that after trying to home, the X and Y axis will now only move in a positive direction, no matter which direction I try to move in. The Z will work OK in both directions.
I reset the program (LaserGRBL) and I even closed the program and restated it again, shut the computer and the machine down and restated them again, but still the problem persists.
I am at a loss to work out what has happened. I guess I wont get much sleep tonight thinking about it.