ryderz,
I think many Plasma problems stem from three things, bad ground, bad ground and bad ground. I remember reading that one guy had to drive 21 ground rods. It didn't work on the 20th, but after the 21st, his problem went away.
It might not help in your case, but I hear Shop Sabre has a new cable that goes between the PC and the Plasma that cuts WAY back on the noise. From what I understand it pretty much removes the unnecessary up/down motion of the torch.
It's not going to eliminate the torch not firing though. I think that problem is entirely removed from the CNC machine or software. Navigator7 is right. It sounds like something linked to the torch itself or its air supply.
Butterknife