I tried removing memory, installing a PCI-e video card, a few more settings in Mach, and BIOS, all with no success.
The old computer was still running an old version of Mach3 that had the old Mach2 driver test. That shows full height spikes on every screen refresh, but I wonder now if those were false spikes. I copied the new driver test over to the old computer, and it was REALLY nice compared to the new computer. No doubt that's the issue. I also put a logic analyzer on pins 2 and 3 for the X axis, and verified the same occasional pauses in step pulses, so there's no doubt that the timing is not nearly as stable on the new computer.
That leaves me with the question of why this is a problem. The driver test program declares that the timing is "excellent", and the motors certainly don't expect the next pulse at any particular time. They would just see it as a speed change, as you have when you ramp up or down in speed. Best I can figure, the motor controller must be the device that's having an issue with this. Not much to do about that really, but I'd bet that another brand of controller might work fine.
In all my research, I've noted that some controllers generate a hardware timer, that's fed back to the software for timing control. Software that uses this clock looks for it on pin 10 of the parallel port, and if your controller doesn't generate it's own clock, you can use a stand-alone board to supply it. Pity that Mach3 can't accept an external clock, because that would be a pretty easy fix to the timing problems.
Bottom line, I can't argue with the need for stable timing, at least in the case of the Probotix motor controllers. It also makes sense to let a dedicated external device handle the chore, as is done with the external timers I mentioned above. In this case, the best option appears to be the SS, so I officially give up. SmoothStepper order placed. I sure hope it works, because otherwise I'll be stuck at 50 ipm.
Thanks for all the comments and suggestions. Now get to work Jeff

Rusty