Hi Henrik ,
If you can really achieve only 13Khz I think you may be having some problem with your drive or the encoder/motor. I is much lower that I have made /and I think I've not made that much /.
And when I say 75KHz I mean encoder steps. With a 25KHz mach3 kernel it means that my M parameter is something like 3 or 4. I tend not to push the computer more than 21-22Khz as it seemes to have problems as slower screen updates and such latency stuff /Driver watchdog triggers also when I got as high as 25Khz/. My CNC PC is PentiumII 733 128 RAM, driving simple steppers so far 3 axis with no problems.
Have you tried to change the board? Or the motor with different encoder? I have experienced some other problems with electronics and found it very useful if there is another equipment to be able to change and therefore compare the results.
Todor