Help! Flywheel/magneto problem

So, after adjusting my valve clearances I take the bike out for a spin. Everything seems ok than all of a sudden I hear screaching sound coming from the flywheel cover followed shortly by stoppage. So, I get the bike to a secluded enough area, come back with tools and proceed to check the rotor bolt (there was evidence it came in contact with the cover. However, the bolt is tight! So, my question is what's causing my flywheel to all of a sudden rub on the cover, when the rotor bolt isn't loose? I just got a flywheel remover off eBay and will take that off and see what is going on in there...Only thing I can think of is that "thefang.co.uk" makes referrences to the starter clutch bolts and how they work themselves loose. Would it be possible for the starter clutch bolts to work themselves loose thus allowing the flywheel (rotor) to loosen on the shaft? Any input would be nice...I've almost had enough of this bike.