Thanks for the comment, Hood. If timing is the only issue, I think a Quad 2.66GHz system should be sufficient to generate three 25kHz pulse streams. Your comment made me try that EMC after all and I have to say I was impressed.
The standard download version let me run the Ubuntu/EMC2 from the CD without actually installing it. Not that I knew much what I was looking at, but nothing crashed and when I was running something called "latency test" it was showing some numbers that seemed reasonable. Plus UMC is apparently not meant to run as a standalone app. The latency test actually prompts you to "abuse" the system to see impact of, say watching a movie, on it.
Comming back to XP was like being hit with ugly reality again. Right after the boot up I was prompet to install that Mach3.sys driver again, which surprised me because I run the Mach 3 uninstall utility before shutting down. That seems to have worked not too well too. It's been many years since I tried Linux and at that time it couldn't compare with XP, but things have definitely changed by now and I very much like what I saw.
In any case, to get to the topic, looking at parallel port setup in my BIOS, it has 4 mode options: Normal, Bi-directional, EPP and ECP, the last one being the default. Could this have anything to do with my problem?