Problems with plasma cutter

Hi,

I have plasma cutter setup on:
Debian wheezy
3.2.0-4-rt-amd64

It has a Mesa 7i80 connected to a Mesa 7i42TA (step generation), plus two other mesa cards for other inputs/ouputs.
It has 4 motors (X axis has 2). According to the users it used to be fine, but all of a sudden one of the X motors lost synchrony. 
I checked cables, motors and step motor drivers, and they all seemed fine.
I realized that the signal was not arriving properly into driver, so I changed the pin configuration on 7i80 from the bad X to Z axis, the problem moved to Z. It normally works fine, however, it sometimes starts failing not only on Z, but also on one X and now also Y (not always but like a couple of times a week). It will star working properly "by itself" after a couple of hours, I do not do much: check connections, change drivers between motors... but it seems to work fine after a while even if I do not move anything.
I replaced BOTH 7i80 and 7i42, thinking they could have been damaged, but the issue persisted. I now believe it has something to do with the computer, linux. 

Do you guys know what could be causing this annoying issues?
Do you think I should replace the computer? 

Any help is appreciated.

I would suspect marginal step/dir signal levels.

How are you connecting the step/dir outputs to the drives?
The only way to get full 5V drive directly from a Mesa FPGA card
is to connect the drives Step+ and Dir+ to 5V and the drives
Step- and Dir- to the FPGA card (or 7I42)