I have a similar problem.
Because of the gearing I need 48,000 pulses per inch, and I cannot reliably drive the main shaft on the lathe faster than 4 inches per minute. As you say above that the motor(s) start to sound awful and they will not run at much above 6 ins per minte. I have fiddled with acceleration - slowing it down so the motor(s) have more time to accelerate, quickening it up in case there is a "sticky" patch they need to get through - all to no avail.
In the end I have put it down to mechanical problems - e.g. the drive shaft does not go through the centre of my table, therefore the pull exerted will be lopsided - my cross slide has a central shaft and I can get up to 6 to 7 reliably on that. In the end it does not make much difference to the work I do, because the lathe is only 2feet long, and most of the work is done around the chuck.
I am going to try some ball screws soon - to get rid of some of the backlash - but it might help the speed.
As Hood said - you might have difficulties with your computer - this you can test by taking a motor off the machine and running it on the workbench. See if you can get above the speeds you are quoting - at least then you will have an idea where the trouble lies.