Okay so I give up with the new PC having tried everything myself and everyone else has suggested to no avail.
So before I cut my wrists I went back to using my original 1.4Ghz P4 PC that use to have the controller built into it.
I now have the controller in a separate box with the power supply and the CNC4PC card. I have bypassed the CNC4PC card to simplify my tests and although I think the machine movements may be a bit better, I cannot get anything reliable out of the machine.
So moving backwards, I took 3 135oz/in steppers back of my Sherline Mill and along with the sherline controller I connected them to my 1.4Ghz PC (the same one the Xylotex board was connected to. The last time I tried the sherline setup I used the PC that the sherline controller was connected to as well.
The results a very good, I can run all axis at 60 velocity and 8 accel totally reliably and the sound good. So this means I can rule out the PC as a problem area, so that leaves me with the Xylotex controller and cabling. To reduce any cabling issues I had already removed my extended cabling from the loop and was just using the cables made up by Xylotex.
I have attached a small quicktime movie of the y and the z in motion with the sherline and I think you will agree it sounds good.
The only other thing to be tried on the Xylotex is the power supply which I will test in a minute with my two PC PSU.
Beyond that I am getting to a point of looking for a different controller, possible the HobbyCNC one which I think I can use with the 425oz/in steppers I recently bought from Xylotex which are 8 wired unlike the 269 which are 4 (Joe can you confirm?)