Hi, I tried searching but can't seem to find the same issue, unless I'm a bad searcher (entirely possible). I also posted this on over at dm.org in an effort to get this figured out.
I've had an intermittent starting and running issue with my bike; it's an 06 S2R1000 with 27500 miles, I've put about 2500 miles on it since I bought it middle of last season with all service records up-to-date, all service done by Ducati dealers.
Normally, it's starts right up and has given no issues. It lives in my barn, so when I take it out, I start it (always fires right up after a few cranks), pull it out, then let it idle on the kickstand for a minute or two while I gear up, close the barn door, etc.
Last week, I did this and after a few minutes idling, the motor just died. It sounded completely normal until it died. I hit the starter again, it fired right up, idled a few seconds, then died. I hit the starter again, and nothing, the starter didn't even turn over. Had to get to work, so I wheeled it back into the barn and took the car.
When I got home, I tried to start it up, it started right up, did the normal wheel-it-out routine, it ran fine and we went for a ride, no issues.
Yesterday, I did the usual routine, after a few minutes of idling, it simply died. I restarted, it ran fine, took it out with no issues for a few hours.
Any thoughts? Only once did it not restart at all, but I'd like to get this sorted just so I don't get stuck somewhere down the line. The unpredictability of the issue is what has me stumped. Thinking about it, a few times last season the motor died as I was getting ready to leave work and the bike idled for a minute while I geared up, but I simply restarted it and went about my day. I didn't give it much thought until last week when it wouldn't restart. This has only happened when the motor's cold to start with.
Other than this, I love the bike, it's great.
If the fuel in your bike was in it before winter you might try running a couple of tanks of fresh fuel.