I'm sure someone with far better knowledge than me will be along soon but for now have you tried setting the program zero at one corner of the machine so that all the moves are in the positive side.
Also do you home the machine every time?
Does it have home switches?
If you've never homed it what are the machine coordinates, if these are a very large number then I seem to remember that it can cause a problem.
Homing is done with the home button on the screen, zeroing to program coordinates is done with each axis button.
You can also check the machine or program coordinates by clicking the machine coord's button, the led should be lit for machine and blank for program.
If you try these and get back it'll be more info for some one with more experience to help.
P.S. You've posted this in the wrong forum, you need to be in Mach 3 if it ends up being a software problem.