I have not had my ST stall while in motion like WJBertrand did, but it does stall on a regular basis when taking off from a full stop (Or at least it used to. I have trained myself to over-gas it at take-off). Pull up to a stop sign, or waiting at a red light, get the green, begin take off, and "huff" it goes right out. It starts right back up, and I head out. I know it is not mismanagement of the clutch or throttle; it's more like the bike is very lean at idle and you catch it just right, and throttle application causes it to flame out. The bike is currently at a Yamaha dealer for this very reason.
Ha! Got a phone call from the Yamaha dealer while I was typing this. Service Tech says they test rode my bike and it stalled on them. They guess, as I did, that EPA restrictions call for lean settings, and that contributes to stalling. Tech is recommending an after-market re-flash. I'm sure many on this forum will agree. I will try to keep you informed...