Hey Phy, that's what I thought too. I went and looked at the fiche for his bike, though, and sure enough, part #32800-37F00 is listed as 'rectifier assy.' There is a sub-note, ' Model K1'(2001) on that part. The wiring harness and cdi are specific to that year also. Over on the magneto page, the stator and rotor are also '01 specific.
It doesn't explicitly state that the rectifier is also a regulator. All I can think is that Suzuki had some idea about a DC ignition in '01 and dropped it again afterwards( '02 and '03 don't have that rectifier).
As far as the magnets slipping? No, you would not necessarily be getting an out of time spark. The trigger(pulse) coil is voltage dependent (hall effect sensor). Even though yours apparently is a dc ignition, the trigger coil is 'upstream' of the rectifier and being voltage dependent needs to be on a 'crest' of the AC wave from the stator to properly sense the timing bump on the outside of the flywheel. The chip in the cdi is also looking for signal in a certain time/voltage range.
That bump can't move. It is welded to the flywheel. The magnets can and do move. A few degrees and the ac wave will be in a null right when the trigger needs voltage. It is not real common, but it does happen. At this point(if you HAVE isolated the kill circuit like Phydeaux suggested), you need to check on the rare causes of ignition failure like this.