Thats what I was getting at. Maybe someone thought they are all the same, but its possible the magnets are a few degrees different. Like i said, this has never happened to me, I'm just guessing. You would have to compare them closely. I would take that bike to someone else, or just keep messing with it yourself. It sounds like you are a better problem solver than the bike shop guys there.
Pull that cover, remove flywheel nut, (impact works the best here) see that the key is in the slot, then I'd pull the flywheel and check timing marks.
I think you can use a timing light , somehow, but again I have never ran into this kinda deal to know how to. Guys running an adjustable aftermarket ignition, may be better reference because they time their engines with a dial indicator. Its probably something to do with that flywheel replacement.