Dial indicator say machine is accurate in MDI screen. But out when

Dial indicator say machine is accurate in MDI screen. But out when
cutting.

Okay. So I have been mucking around with my plasma/router machine. I
am trying to get some positional accuracy out of it. It is maily just
a CNC plasma table. I put a router in it so that I could take more
accurate measurements, as measuring a plasma cut part has other
factors to deal with.

So I have been cutting MDF. I tell the machine to move 100mm but it
will be out. I clamped my dial indicatior to the frame set it all up
at 0 etc. Went into the "Set axis steps", the automatic thing. I
tell the machine to move 5mm. After a few goes I get it spot on!

I can then go into the MDI screen and tell it to move 5.00mm and it
will move the 5.00mm. Then I can go forward another 3.54mm and it
will do that fine. Then tell it to go back to 0, and the dial
indicator will be spot on the 0 mark.

But. I go to cut a bit of MDF with the router 100mm long and it will
be the incorrect length.

What bugs me is that it is working in the MDI screen, ie move 10mm it
will. Even move 300mm and then back to the 0 the dial indicator will
be on 0. I was impressed with this.

So, after a bit of reading here ther and everywhere, I decide that it
could possibly loosing steps when the router is cutting. So I slow
the acceleration down. This has no effect. I'm using two 1200oz/in
steppers slaved one either side, then they are belted down. I am only
cutting at about 500mm/min at a depth of 5mm. So there is plently of
torque from the stepper motors etc etc. So I think that I can rule
out the missing stepps theory.

But could it possibly be electrical interference causing my troubles?

Have a look at this picture, this is my power supplie, breakout board,
stepper drivers etc. It is very messy... etc etc.

http://i90.photobucket.com/albums/k259/peterapalais/electronics1.jpg

http://i90.photobucket.com/albums/k259/peterapalais/electronics2.jpg

What are the chances that this birds nest is causing me trouble? ie
20% 40% 60% chance of electrical noise etc.

If so, what is the solution. Make up a new board and space everything
right out so that things are further apart? Should I use sheilded
wire etc? If so for what connections.

Cheers
Peter
Australia