Hi Robin,
I did pull up the task manager and took a screenshot of the processes running, and nothing stood out as odd. I'm at work so don't have this picture, but will post it later in case anyone spots anything. I didn't try the CPU useage graph, but will have a look.
In terms of Mach3+windows, I know there are many happy users running this combination so I should be able to get to the bottom of this, although I accept your point about Linux.

FatFreddie,
I'll have a look at EMC2 as part of the investigation. Should tell me where the problem is/is not. I ran the Mach3 test for about 20 seconds, and Mach3 was minimised and not cutting, but nothing else. I should try this with more things running, and for longer, and see what happens.

I'm working on a way to capture the scope data since this would be a great help. Once I get the stepper video posted on youtube (never posted video before), it should help some of the experts out there to offer a solution.

Another thing I'm going to try is to look at the signal off the parallel port directly at the motherboard. My scope data was from the end of the parallel port cable. I have read about suspect cables, and I'm hoping it is as simple as that because it would be easy to fix!

Thanks for all the suggestions so far, there are more things to try than my hobby time allowance allows (don't ask!) but I will get through them all in the end.

Thanks
Barry