X- Axis won't do as it's told

Hi Gang,
I am slowly going bald here as my router has been playing up on the
X- axis ever since I first built it and I am pulling my hair out at
an alarming rate.
I am using Gecko drives, 24 volt supply (36v), 20,000uF Cap and all
the usual stuff crammed into an old computer case. I have tried
Master5 and CNCPro and Kelly Cam with the same results on all
programs. This is mark2 of the control box as I thought I may have
been getting extraneous RF pulses through the circuit causing it to
malfunction. I had sheilded the control cables with Al foil and
earthed them at one end without any effect.
My problem is that the X-Axis is very unstable and has a mind of
it's own when it comes to the direction I want it to go. Sometimes
it goes right then all of a sudden it goes left and may go that way a
few times then back in the right direction. I had it running
smoothly 2 days ago and thought I had tweeked it the right way but
the next day upon startup it behaved erratically and roughly again
with no intervention on my part. I have tried to slow the pulses down
and also set the acceleration to heaps of different values.
I am now on my 3rd motor as I have tried 3 size 23 1.8deg different
value steppers 4 wire and 6 wire and I am now using a size 32 2deg
stepper. ( my last as I burnt the last 2 out trying different values
for the resisters)
My router has linear bearings on round bar and 3 start 3/8 acme
teflon coated screws with plastic nuts and runs very smoothly when
turned by hand with no power on and very little friction so I am
positive it isn't mechanical.
The Y and Z axis run very smoothly and I have tried swapping wires
around using the drive of another axis but still have the same
problem. Even went to gearing the drive down with toothed belts
about 3 to 1 for more power. I am nearly convinced that I am doing
something wrong with the speed and acceleration settings in the
software but nothing I try seemes to work. Should I uninstall
everything and reload the Progs from scratch?
Before I fitted the 32 stepper I had a vexter 1.8deg 4V 1.4A 4 wire
motor fitted which ran very smoothly but I always lost a heap of
steps when doing a project. Sometimes 0.020 in an inch but mostly
just enough to cut out the side of letters when cutting a sign. It
was always smooth going right but lost steps when travelling left.(I
even tried turning my nut around to face the other way). That is why
I went to the larger motor for a bit more grunt just incase things
were too heavy for it but the problems seems to have worsened. (very
stuttery and unsmooth)
I hope I have given you enough info as I am getting a churning
feeling in my guts and the 14lb "linear rectifier" is sitting next to
the router for some serious tweeking should I not be able to work
things out. This has been going on for 4 months and I can't seem to
find anything in this list that has helped yet and I have scoured it
nearly every night in that time. This list has been a godsend for
building my machine and it is so frustrating to be so close yet so
far so I hope an angel is out there watching over me that can help.
Warm regards
Richard.