I don't know about it being the OS, Mach 2 runs under Windows 2000 or XP and I can get 180 IPM, which works out to 45K pulses per second. This can be handeled by all 6 axis.
did you take the time to go through all the setup steps?
A fair amount of MACH 2 users forget to set the units to inches, so the machine travles at a max of 180mm a minute. I've had them on the phone when they change the setting and then WOW.
Just look for setup stuff like that, you might also want to try the CCED yahoo list.
Thanks
Aaron Moss
www.IndustrialHobbies.com