If you are having any trouble with the second Parallel port, that is a big red flag and you may have a conflict in the computer. Check to see if the two parallel ports are sharing and interrupt or have an address conflict. IBM defined these many moons ago, but add-in cards often come pre-configured as LPT3 (and LPT4 plus COM3 etc, if it is a multi card) or otherwise break the rules. It may be that you are chasing a problem in wiring that the PC itself is generating internally.
I can tell you from experience that bad, cheap or failing PC power supplied can make a horrific amount of noise. So much so in some cases that you can actually hear it in the motherboard speaker!
Use the task manager to check the CPU utilization. If it maxes out, it probably would not be a good thing with such a timing sensitve application as Mach. If another process is runing with a higher priority, it can suspend the lower programs. Also check to see if you have antivirus or a similar 'watcher' program running which could be intercepting the LPT1. Parrallel ports were often used for file transfer and networking at one time and it is possible that security software is monitoring it.
The only other though I had was based on my recent discovery that a wireless network adapter was making the whole CNC go nuts. False estops, false limits, and the steppers would suddenly stall for no reason. Unplugging the USB wireless adapter made ALL of the problems go away instantly.
Something else . . and this may be a stretch . . is if you are in an industrial area where some company has radio dispatched trucks. If you are getting slammed by a powerful transmitter, it would probably behave exactly like you are experiencing because it would all look fine until someone keyed the mike and it would just be an amazing coincidence if you happened to be looking at your scope at that moment.
I am still a newbee at this stuff, but still, I would put a spotlight on that PC as a possible suspect.