I've had this same thing occur on my 1090, 4x now. It has happened both before & after installing my Arrow headers/mid-pipe (stock ECU, no remap). It happens when decelerating (closed throttle) & down-shifting from 3rd to 2nd, the bike just quits. It has happened on 3 occasions at the early stages of a ride, even though I typically let the bike (which is on a battery tender) warm up for several minutes before I take off. It also happened once after riding all day. There is no aftermarket alarm system fitted.
I came across this reply (Thanks jonadd) in one of the posts & thought it made good sense as to why this might be happening.
Cheers,
Glenn
http://www.mvagusta.net/forum/showthread.php?t=48125
"Ok, some issues. I read the entire stalling thread, and decided the issue was mostly riding style/technique. Being a trials rider I aspire to precise throttle control, and pride myself on being a smooth rider. I removed the external throttle return spring, and I always roll the throttle back against the stop before pulling in the clutch on decel. Those changes alone have all but eliminated stalling. I stalled 6 times in first 50 miles, 3 times in next 800+ miles, 2 of which were my omission, only one due to a stumble at idle. Idle still stumbles every now and then, but not often and usually not enough to stall.
Note I am not giving her gas with the clutch engaged, just holding the twistgrip back against the spring pressure. I like to use engine braking, so I decel hard in gear and she never stalls under those conditions, only with the clutch in and revs falling down to, and past, idle rpm. I have ridden a few light flywheel, highly tuned motorcycles with fuel injection throttle snatch, so I think in terms of rpm momentum, and just don't let the rpm's fall too low too rapidly with the clutch in. Mostly, I accept the fact that I bought an exotic racing derived bike that offers incredible performance at the expense of some relatively small drivability issues. Others may have greater problems with their Brutales, but for me on mine, stalling is a non-issue.