Update,

Installed ISO recorder into windows xp, and created a proper boot disc for Ubuntu and EMC2. Installed this onto a reformatted second HDD. I ran the latency test and got max jitter servo thread of 6983, and max jitter base thread of 7541. These are similar to the results in the EMC2 manual, so assume are OK.

I then ran EMC2 using the 'stepper mm' profile. Unfortunately this also glitched the motors!

I then tried the profile which sends the stepper pulses to the speaker (nice feature). This also glitched. I attempted to record this into another computer using 'windows sound recorder', so I could post this and do some analysis on it, but got the windows error about not enough memory. Microsoft say this is a problem on machines with more than 2GB (this other machine has 4GB), but do not offer a fix.

Anyway, later today I switched on the CNC PC and tried Linux again, but system will not get past POST with 'NTLDR is missing' error. Tried lots of things but can't get past this. PC obviously thinks there is a problem with the boot or root directory of the Linux HDD.

Went back to Windows XP and added a PCI parallel port, added the driver, and configured Mach3 to this port. Motor rotated, but still glitched. Glitches are still happening at <900mm/min or so, but not >1500mm/min. This test probably means the built-in parallel port is OK.

So in summary:
Fresh install XP, optimised computer (all drivers updated, standard PC, minimal hardware enabled etc.): this helped and glitches only occur <1500mm/min
Brand new replacement driver system3 board from Roy - glitches
Mach3 using PCI parallel port (Moschip) instead of built in port - glitches

Fresh install on reformatted HDD of Linux and EMC2 - glitches
Linux and EMC2 output to speaker - glitches

This all suggests it is the motherboard (ASUS A7N8X Deluxe Gold), or MB chipset. I would welcome information on successful MB & chipset combinations which work with Mach3 (or EMC2), what are other people using?

Also, been reading about smoothstepper. Since this takes the timing away from the PC, do you think this would help?

Thanks
Barry