Did you check the steps for the system? They might have to be adjusted. Using a calculator is a good starting point, but you have to take into account the design differences in your moving parts. For example, my leadscrew on my small machine was calculated out to 200 steps per revolution, but in actuality, it was 193. That extra 7 steps made the machine 5mm off over 600mm of travel.

I would look it over and check your using servos or just at the GCode for the steps of the machine. If using mach3/4, go in and do a calibration on the motors.