Missing pulse problem

I have a program which controls a 3 axis X, Y, Z machine via the parallel port. In order to have more computer time to do necessary calculations, I am sending an external 1 KHz pulse into the PPT, the program responds with a series of 1 to 31 pulses for each of the (3) axes representing relative speeds for each axis. (The max resulting pulse rate will be 31 KHz.)

The external circuit accepts the respective parallel data for each axis and generates a smooth train of pulses to drive stepper motors to run the machine. My problem is that there are missing output pulses in response to the 1 KHz clock. On careful investigations, there are exactly 15 missing pulses every 10 seconds (or 1 1/2 pulses missing per second). I can even view the missing pulse on the scope, although it is difficult.

I have tried removing the mouse, but no improvement. Each of the (3) computers I tried this on produce the same results, and each has WIN 98 as the base program. I switch to the DOS operation before running the program.
Another effort was to startup using a DOS startup disc, but still the problem. I am losing 1 1/2 pulses every 10 seconds and this is unacceptable.

Is there some resident housekeeping interruption in DOS??
Or is this a carryover from WIN 98? Should I completely remove all traces of WIN on my hard drive and use DOS 6.22
alone?

Hope someone has some good suggestions!
Thanks,
Jack C.