Originally Posted by 20valves
I fixed mine by twisting the throttle past 20% during significant altitude changes,
That doesn't fix it, it makes it worse. It was really annoying having douchebag service rep types tell me that over and over. It turns out the software only updated ambient pressure every so often, and when you rode aggressively in big mountain terrain it quickly got out of whack very fast. Stalling repeatedly when you'd try to pass or give it some throttle etc. However if you stopped and shut it off sensor would reset and you'd be good to go for another 1000 feet or so. Bike was unrideable where I lived at the time, would ride from 6k ft to 12 k ft often and hard.
About a year later after a lot of back and forth with Yamaha, I got a letter about an updated ECU. Fixed the problem and has not come back.