You could try the EMC2 trial disk (http://www.linuxcnc.org/content/view/21/4/lang,en/) which would help determine whether it's hardware or software.

It's interesting that Mach3 appears to think the PC is ok but there are problems in operation. How long did you run the test and what other system activity was there?

The EMC2 latency test suggests running it for a while and stressing the system at the same time.

Will the scope capture to a file? - it might be more instructive to see a series of pulses.