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There are two other parts of the starting system that might cause problems.
Possibly the air temperature sensor is playing up and giving false readings?
Also, if the 796 is like the Evo, then there will be a stepper motor, which, according to the manual, "...defines the magnitude of the supply of supplementary air, down-line from the throttles, during the engine starting phase.
I don't know how you could check either of these components without plugging in to the Ducati diagnostics but I'd have thought you'd see an error code if they had failed.
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