Never crank a bike with electronic ignition without grounding the plugs or you will fry the ignition.
If you have an M1100 with Siemens ECU, take it to the dealer and let him hook it up to the Ducati computer for that cold start. He can see what is happening to cause one cylinder to fail to fire. A compression test won't tell you much about that!
Your EFi is a whole lot more complex than a carb bike with points.
It's even possible, though unlikely, that half of your ECU is faulty. This is not a DYI diagnosis IMO.
Thanks for the red-flag, Curmudgeon. While I have cranked over EI Kawasakis without ill effect, they did not have the ECU that the Ducks do.
Oddly enough after sitting two weeks (I have been restoring a 67 Comet, and the bike was buried in car parts) it roared to life on the first stab this morning and ran great. Almost took the long way into work it felt so good. But, you are right: I was thinking old-school, and with the ECU tracking everything it should log "something".
Thanks for the response!