I've been having this problem recently since it has gotten colder. On cold mornings I can hear the fuel pump when I turn the key, the engine will turn over when I hold the starter, but it just does not start. After a while it will show fault code 11 and the engine light will flash as I'm holding the starter.
If I try later on in the day when it warms up outside it will start no problem, even if the fault code 11 is still showing from the morning.
This seems to happen when it's under 45 degrees F outside. Bike only has 7100 miles.
I actually had this same problem around the time I bought the bike in April: http://www.r6-forum.com/forums/showthread.php?t=157114
It happened a couple times then but I'm now realizing that it is due to the cold.