Not a lot of information here as yet, more information will be added over time.
This problem was reported to dealers under TSB for a range of dual spark VIN's but has been observed in some earlier single spark machines as well.
Some gearboxes were assembled without the thrust washer (# 7) being installed on the gearbox input shaft (clutch shaft, # 2). The result is an irregular, metallic knocking noise in neutral, with the clutch engaged. This is due to the dogs of the gear wheels of the 3rd and 5th gears (#s 6 and 9) knocking against each other.
Place machine on sidestand in neutral and start engine or rotate rear wheel. To repair, dis assemble engine and fit the thrust washer. Riding with the gearbox missing the thrust washer will not cause damage or affect operation.
Plastic cages are used in the crankshaft bearings and plastic is also used in the oil pressure control valve and the insulating washer for the gear selector drum. Higher than normal oil levels result in these components being submerged in oil which they are not designed to be. Engine overheating can also cause damage to these parts.
1st Gear/Neutral cant be selected but 2nd to 5th gear can be selected.
Pin to the neutral switch may be bent.
Excessive oil in the air intake system
Plastic gears of the coolant and oil pumps,
Plastic mushroom heads of the oil pressure maintenance / control valve. Part No 11112343009 (Behind Oil Filter)
Crankshaft and all plain bearings that use plastic cages (except the gearbox output bearing)
F650CS Only - Y piece at the connection between the two sides of the oil tank.
Engine Oil filling procedure from 650GS/650X owner manuals & TSB Oil Filling Procedure PDF
The Gear Lever Seal & Clutch Arm Seal can both wear and leak requiring replacement.
The neutral switch is on the RHS behind the front sprocket cover.
The neutral switch plastics can age and break, plus the pin can bend.
This can cause poor gear shifting or even prevent selecting gears.
It may be worth checking the switch periodically.
The neutral switch threaded section is 10x1.5mm, 20mm long
Out on the road an emergency repair for a bent switch
Remove the switch and cut off the switch section to use the plastic threaded part as a plug to continue riding. The danger is the insulating washer on the selector drum may be broken and fallen into the crank case.
Neutral selection problems may be able to be resolved by placing a washer under the head of the neutral switch
Sealing the connection with a dab of silicone is also worthwhile to prevent earth leakage in wet weather.
The front sprocket retention system is different F Series and G Series.
F Series has a 30mm Nut (M20x1.5 thread) and a locking washer.
G Series has an M10x35 bolt (17mm Socket) and locking ring.
The raised section of the sprocket goes to the outside.
There are at least some G650GS which dont have a steel bushing in the clutch cover which causes problems in clutch release and first gear selection. 2007-08 G650X are also affected. See the pdf for details. The links page has a link to the original G650X write up on the problem. G650GS Clutch Release