This does sound strange. I guess the first thing I would do is make sure that the fly wheel is completely seated when tightened down. But that is kinda obvious. Maybe the keys arent seated properly preventing the fly wheel from fully seating on the taper. Are both engines the same? IE: both long or short shaft. Just pulling straws here. Assuming the seating is ok I would pull the fly wheels off, mount the engine in a test stand, pull the plug and rotate the crank shaft to check for any wobble. Hard to see a wrong cut on a hub or the flywheel when done on a lathe. I suppose its possible but I cant see Peter turning out something like that.
Edwin