Hey Fabiano,
I have a few questions. You keep saying PPR. By this, do you mean steps per revolution or steps per unit? Are you set up in inches or mm as your default unit? I assum mm. Do you still have the steppers hooked up or the servos? What is your gearing for both set ups? What drives do you use for each, microstepping? If so, how much, 10, 8,2? Can you post both XMLs? Have you tried it at 25KHz? If you go to a higher pulse rate in Mach, do you reboot and does it stay at the higher pulse rate after you reboot? Can you run a driver test and take a screen shoot?
Brett