Set the active offset X and Y values to 0.000. Or better yet, reset the X and Y axes to 0 at the material zero point (front left corner). Mach3 will automatically calculate and update the G54 offset to be correct for this part. Also, check the DRO on the Run Program screen. If the "Job" DRO shows X3.000 when you know your physical tool is at the X0 position of the part, then the G54 offset is active and set incorrectly.