Hey Bill long time.........
If you using steppers, they loose power at thier higher RPMs, so mabey they are not large enough for your gantrys wieght at the higer rpms...
check you pulses on an O-Scope at the higher rates, see if you getting a consitant full 5 volts, if you see some fades here and there, that might be the voltage falling below what your drive needs to see, and it misses the pulse.
lastly, it could also be your computer might not be able to keep up, at the higher rates of pulse, it may make a DMA access that puts a "Hickup" at your higher rate.
check your hard drives and see if they are making DMA access or some other program(s) are.
scott