First off I'd check your jog settings in the dialogue box (pressing tab on keyboard) and see if it's all at 100%.
If I'm doing say a manually fed face skim I drop the speeds via the jog box. Sometimes forget to put it back before next use.
Easier than changing all the motor velocities.
My Mach 3 is also off slightly but nothing like yours (only about a 20-30mm/min difference) never figured it out.