I'm probably way off the mark but............. could storage of the bike / leaving the bike running for extended periods on the side stand contribute??

Not in my case. I always use the centre stand and never leave the engine idling for any length of time whether upright or on side stand.

May I suggest those with highish mileage check for any play on the primary shaft. Can do this just by removing clutch cover and turning clutch back and forth.

500 miles after rebuild (bearing only - crankshaft was ok) knocking and vibes returned.
The plate washer had worn causing the primary drive nut to be loosened.

Maybe 50 ft/lbs is not enough (edit: 58ft/lbs!). I did it back up to 60 ft/lbs and the bike is running better.

Interesting how the XT600's nut is quoted as being 80-90 ft/lbs in different places.

The plate washer has a coating which wears off due to it spinning between the bearing and balancer drive gear. The cause of corrosion and loosening of the primary drive nut??

Update.

Recently replaced the plate washer and primary drive key and torqued the primary drive nut (which was loose again) up to 65ft/lbs. Would have gone further but didn't want to push it with the manuals technique to hold the crank (strip of aluminium between the balancer drive & and driven gears).

A few hundred miles later and I'm wondering how long my Ten can last before it needs it's third crankshaft.