Hi There
I also have an 09 R1 and started to notice the very same noise that your talking about. At first i thought it was big or little ends lacking lubrication as after a second or so of running, the noise clears and does not re-appear all the while the bike has been run very recently (same day etc).
All in all, not good!!!!. Now i have seen others with this same problem, i will phoning the dealer on Monday with a printout of this forum.
Has anyone else contacted there dealer and had any feedback, would be very grateful if you could let me know ASAP.
All the best Tony.