Stutter in Stepper Config moves

I'm building a gantry style mill/router and have found a problem with the pulsetrain while testing an axis.

After setting the step and direction output parallel port pins and in the x-axis setup screen I tell the axis to jog or cycle back and forth. When doing this, there is a stutter in the movement when ever I move the mouse, type a key, or when anything on the screen changes, including the blinking cursor.

The pulse timing is set to the L297 setting (it's an L297 based stepper drive) and the minimum scan time of the compter is 25000 ns. Changing this to 50000 ns, doesn't help.

When running the latency test, the max jitter is around 24000ns no matter what I do, including much typing, mousing, and asking for all kinds of openGL graphics while playing a video.

I don't think it is electrical noise because how would the blinking cursor make the difference in the noise from the video signal. I'm guessing it is some kind of interrupt of the PC that the latency test can't see.

Can anyone point out what I'm missing?

Thanks in advance. Chief Geek

I'm not sure how much it exercises the software but you might try to use the
stepper sim_inch configuration. You could then manually jog and listen to
the PC speaker to try to hear discontinuous tone. What step rates are you
using?