Bike: '05 999 S (yes, the fast year)
Mods: Termignoni slip-on, Corse air filters
Mileage: 11k km - 7k miles
Behaviour to this point: Flawless
Service: 10k done - no issues. Valves fine.
The bike starts instantly when cold. Go for a ride. Stop for 2 minutes and it starts right up. Stop for 10 minutes and its struggling to start. Cranks over hard and fast (for a Ducati). Battery fine. Not touching the throttle or the choke lever while trying to start. Runs strong when it starts which is usually after one cycle of the "auto-start" system. Plugs look good although they were just changed at the 10k service.
Now, I've been a good litttle Ducati owner and bow towards Borgo Panigale four times a day so I'm not sure what I've done to upset Dr. T.
I had a similar problem on a fuel injected car once. Then it was a non-return valve in the fuel pump that was leaking, causing the pressure to drop in the fuel line and fuel to evaporate in hot places. Once you get bubbles of gas formed fuel in the fuel lines you get the behavior you describe, and it's only when the engine is hot. Once the engine gets cold again fule goes back to liquid form and you'll have no problem starting the engine.
I would remove the fuel pump assy and check for cracks in hoses and plastic parts inside the fuel tank.
Sorry if the explanation is confusing. I lack some English technical terms here!
It's vapor lock in the fuel system due to heat soak when parked. If you have alcohol in your fuel blend it exacerbates the problem as that crap boils easily.
Try this first. Turn the key on and let the system pressurize. Then key off and wait about 5 -10 seconds. Key on then go for the start. Sometimes this burps the vapor out and it'll fire right up.
Cure:
Wrap the fuel lines in mylar coated nomex fire sleeve. This reflective insulation and nomex will shield the hoses where they cross over the hot engine. Worked well on my 998 that had the same embarrassing problem as the hoses go right on top of the rear head cover. There are no hot start issues now. Get it at a race car shop for about $20 and you'll need about 1.3 meters. Clicky the linky.