Can my CNC controller blow my motherboard?

I have a problem and am looking for advice. I have two motherboards
fail on my CNC setup and am starting to suspect the controller. The
first MB just died. Would not boot. I have no idea why or when this
happened as I came in one day and it would not turn on. Got it
replaced under warranty. Replacement MB lasted about an hour and the
keyboard quit working. Now when it boots, it sounds like a stuck key
error (clicking) and computer says no keyboard present. I have tried
3 different keyboards both USB and PS2, but none works.

Can there be something come back through the controller to cause this?

Here is my setup;

ASUS TUSL2 Motherboard.
Running Mach1 software.
Super-tech Servo controller (Gecko 320's) Model #EMC-XYZGS-BX

I have talked to the controller MFG and they claim there is no
possible way that it could blow the MB.

Can I buy something to protect the parallel port in case there is
something that can come back to kill it? Is there an optically
isolated parallel port card or something that could protect me?