Ok, so for those who don't know, the solution to my X axis only stopping on one side when homing is this...
"Regarding master and slave axes - the device is designed in such a way that separate home switches are expected on both master and slave axes. If this is not the case, the common switch must be wired to both home inputs (of the master and slave axis) in parallel and configured identically."
Hope that helps someone out there.
The VFD had a short circuit... one on the shielding on one of the cables was touching the cable and shorting things out somewhat, Just stripped it back a little and all good.
Also the shutting down story, I changed the usb to another port and that seems to have fixed that, i was wrong thinking it was to do with the vfd and switching on the spindle on, is was a loose usb connection. when it lost the signal to pokeys it shut down, still not too happy about that tho.
PoKeys support have been pretty good, I'm going through a crash course learning mach4 and pokeys and they have both been patient with me.
Any one have any ideas what this is all about...
https://1drv.ms/v/s!AvolCJeAoVyswzHJ_k6cuQfk5prQ its a video showing the steppers stammering somewhat. it happens to all the axis and is quite random. its not losing steps tho i am still tuning the motors, this stopping/interruption/stammering thing has me baffled also.
one day this will all just be easy.