I have had my F650GS since October 2008 and it has run perfectly.
It's unfortunate that some are having stalling issues. I'm not a mechanic but if a few bikes are haveing this issue maybe it's not the bike but the fuel. Could you have gotten a dirty tank of gas or maybe water in your tank from condensation (cold outside, and storing the bike in a warmer garage causing condensation)?
I live in Southern California where the temps don't go below the low 40's. Riding in cold weather might be causing condensation. I would drain the tank completly and then fill up from a national brand gas station that appears to sell a lot of gas. The water in the gas might come from a gas station.
Just an other way to solve your problem. Good luck!