without going into too much detail, I would check two things first:
1. lines of code: did you reinstall the mach3 licence when you reinstalled the controll? Without the licence the controller is limited to a certain number of lines, I think it was 500.
2. There is a setting for incremental vs. absolute dimensioning for for circular interpolation I think it is on the settings tab. Make sure you have set the right setting there. Mine was on absolute when I first started it up.