Within the Mach3 directory there's a file called "drivertest.exe". Find it and run it and test the quality of your parallel port signal. I had a nearly identical problem trying to run Mach3 from my Dell D800 laptop, and learned the parallel port quality was horrible!
I bought a SmoothStepper and cured all the problems.
In other words, in my opinion your problem is signal quality, from your computer. Run that file and take a screenshot (Alt+Print Screen) of the window while the test is underway.
By the way, the cheap parallel port emulator cards will NOT work, save your pennies and get what you really need They provide enough signal to run a printer, but not a CNC card. Go to http://www.warp9td.com/index.php to read up on the cure.