Could it be that the cause lies in a loose nut, the one that holds the balancer on the crank in place... seems to happen once in a while...
... which might have result in a worn out crankshaft bearing after so many miles unbanlanced operation...??
... just speculating...
but check this topic:
http://www.xt660.com/showpost.php?p=141935&postcount=15 also at about 50.000km.
This is what it sounded like:
http://youtu.be/rjYYt1DstIU
EDIT: on a second read of TS first post I noticed:
and discovered the primary drive nut was loose (tab washer still in place) ... so yes ... it seems to be the same cause...
Niek (the one of the videoclip) decided not to ride with the bike and had the dealer fix it. All done and his bike has ridden another 50.000km's since...
HJ