Interesting, I have a 2011 990 with the exact same symptoms. Bike runs perfectly under power, on decel, overrun, etc. But every once in a while, if stopped at a light with the clutch pulled in, when rolling on the gas the bike will pop/fart and then stall. It'll start right back up and run like mad, but the occasional stalling thing has me stumped.
Sync'd the Throttle bodies
Set the TPS
Checked the Map (Powertripp)
I will be:
Checking the valves this next service (but they were fine at the last check)
Replacing the plugs
I'm running a foam filter now, but the issue occurred prior to the new filter. I've just started rolling on the gas harder/earlier from a stop. It's a band-aid, but I haven't a clue what else to check.