The extruder on my printer is about 34mm offset to the right. It homes the X axis fine, but when moving the extruder to 100 on the x axis (200mm^2 print bed) it is slightly off to the right. Is there a way to manually change this? Larger prints fail because it will just extrude plastic over the right side of the bed, thinking it is centered. I flashed Repetier frimware to the printer so I can use filament that wasn't DRM locked by XYZ, so that is probably why the preset DaVinci profile didn't work.
That means that you probably have some incorrect settings in the Repetier firmware. The machine obviously hasn't changed, and the commands that S3D is sending haven't changed. If you re-flash the firmware you need to make sure to set things like the homing offsets and build dimensions correctly. Otherwise, the parts won't line up since the firmware thinks it's in the wrong position.