Just a heads up for anyone with an 06 R1.
I took the bike in for a valve check before the warranty expired and the fact that the bike had 47,500 Kms on the clock.
The bike was running normally had and had regular amsoil changes and all scheduled maintainence.
Got a call to say that all the intake clearances were large and that several of the shims were stuck. It turns out that some if not all of the intake valves had mushroomed at the tips, allowing the shim to fall.
Yamaha are replacing all 12 of the intake valves. The valve seats, both intake and exhaust are fine, there is no noticeable wear on either the cam lobes or the buckets and the cam chain and tensioner are fine.
There had been no change in noise from the engine and the thought is that this may have happened early in the life of the engine.
Might be wise to have the valves checked before warranty runs out no matter what the mileage.