Hi mac,
The moving knot pulley system was removed for the last few tests and the issue remained so it isn't this, I'm pretty sure something is interrupting in software. I don't think mach is at fault but rather some background process. I will try to test as you say, thanks for the advice. The major change I made to the X during rebuild was tensioning the belt a lot, I may reduce it a little too as it was working well before.
Racking is possible but I will have to check, ideally a slave motor would be great and I will be doing that, at the moment I can't really afford the build time to do the mods at the moment.
If you look back at my wiring pictures, do you think having the Y stepper so close to the controller could cause problems (magnetic interference?) just a thought.
The other culprit could be noise or poor circuit design on my controller pcb I can isolate reliably with the digital storage oscilloscope so il try that too. I've had issues with boards and slow optical isolators causing missed steps before. Thanks for the guidance, appreciate it. Back to it....