You should probably make sure the throttle bodies are set up correctly: Throttle sync, cable freeplay, etc... The air bleeds should not be shut all the way. This is likely masking another problem.
Do a search on throttle set up (or similar), as there is some good info. I believe member BradBlack maybe? had written up a good how to http://www.ducati.org/forums/1098-1198/20317-throttle-body-sync.html?highlight=throttle+sync
Not the link I was thinking of, but helpful
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