I believe calibration *HAS* to be done once you receive the machine. It's not explicit anywhere in the original manual but it's "obvious" to me. Things move in any CNC. People with big lathes or mills either have a special operator / technician or do it themselves, but generally, after leveling the machine (takes ages), you go into calibration for a few *days*. Fortunately, it's simpler and faster for that PnP machine. However, it's not a cast iron bed neither, so it's more prone (IMHO) to variations after shipping etc.
Overall, mine wasn't that bad. The main issues were the camera-to-nozzle offset and the parts offset (4 orientations). Once I got that right, it was 95% of the calibration done. The rest was scales to be slightly corrected and some axis.
I just do what you do. I have templates, some of them with empty PCB data (just the feeders & trays data), or sometimes I'll reuse a PCB, save it under another filename, delete the PCB data except the fiducials that I only relocate, then start populating the board again. I never got your issue. Again, I would check the file with an hex editor, just in case.bmw330i wrote: What is the best way to copy an existing board. Meaning I have a board that's very much like another board. I'd like to duplicate the one and just go change the placement values. The parts are almost the same between them.
I would also email MDC with the program file attached so that they can have a look.