My new twin F650gs didn't give me any problems until I got in horrific wind and rain. It would not only stall downshifting into first and second, but also at high speeds usually when shifting up to sixth gear. I was on a three day trip, and realized it would stall every time it started raining, but would run fine when the weather cleared.
I took it to the dealer, and they did a software upgrade, but I am not sure if that will fix it. That same day a F800gs rider came in complaining of the same problem. He didn't have any problems either until he got caught in the rain.