Did you ever set the pulley speed in the config/spindle pulleys section of Mach? It took me forever to figure that out - since I never use any other gear speeds other than High/3, I never set anything thinking it wouldn't matter. However, even if you only use the high, you still have to set the pulley speed (3650 or whatever your motor is) so mach knows what is max. Once I did that, everything worked great with the cnc4pc card and I could use the recommended values and adjust with the pot on the cnc4pc card.
Try that and see what happens. From my understanding, the Step Pulse in the motor tuning (probably what you changed) is what the CNC4PC card uses to convert the step pulses to proper voltage - the higher the number, the higher the voltage -at least to a limit. If that is what was changed, I could see your spindle going crazy if it was setup properly then that number was adjusted.
As for rapids - I've had plenty of issues, so I now run mine at 80, 80, and 60 (x,y,z). It was the only way to not fault out. Granted, I'm going to upgrade to bigger motors to at least get me up to the 120 range, but I've learned to live with the slower rapids just to have the reliability.