I've had it happen; seems like turning the key back to off stops it on mine. Do a search if you want more info - it's out there...

 

probably the soleniod sticking.

 

This happened to me when I first got my cycle from the dealership but hasn't popped up since.

 

Ducs seem to have a variety of starting issues....
'Dane, I think you have (A) :

A) On late model Monsters with the 5.9 ECU, the starter button sends a voltage signal to the ECU, which looks at a group of sensors (neutral switch, clutch switch, sidestand switch and maybe others) and decides whether it will allow the starter to crank. My '02 S4 has done the same thing as yours did. Cranking, but no start. Do a key off/key on cycle, and everything is fine. I'm pretty convinced this is a bug in the ECU software.

B) Sticky start button. Usually cured by a clean & lube job.

C) Sticking or non-functioning starter solenoid. The OEM starter solenoid doesn't seem very robust, CaCycleworks has a replacement unit that's a lot better. A real PITA if it sticks, 'cause the starter motor won't stop until you disconnect the battery. If the bike starts and you don't notice that the starter is still cranking, it can stay on for a long time...Very hard on the battery, solenoid and starter, they're not capable of continuous duty (no starting system really is).

D) Wiring continuity issues, from the switch all the way to the main power cables to the starter.

 

Mine did this once with only 1000 miles as well, hasn't happened since and I'm at 5000 miles.

 

This is fairly common on new Ducs, goes away quickly. The starter button can also get crudded up on older ones, especially when stored outside or not ridden awhile.