The 5V usually goes via the charge pump relay to the enable signal. This is to prevent the outputs from activating when Mach is not open.

KTM

But I still cant get the motor to turn!

Regarding the square waves - What is the amplitude and frequency - are they only active when you run the g-code.
you can also run the motors from the manual screen - press "tab" on your keyboard.
Try adjusting your feedrate - maybe it is far too slow(unlikely)

KTM

Not having measured the amplitude and frequency I dont know, they are only there when I run G code and do start and stop. I did notice that it looked like 3 traces running in parallel, but I am not an accomplished oscilloscope driver.

I have gone back to basics, I have stripped a stepper driver out of the box, I have stripped the cable off of a motor, I have stripped the breakout board out of the box, completely rewired them and I will try it on a bench power supply tommorow.
Now I am going to have nice meal and a glass of wine.
Thanks very much for your help. I am sure we will turn over the correct stone in the morning.

My wife thinks I am a bit grumpy at the moment cant think why.

Clive