Sometimes the little things are the hardest ones to track down. Living in PA we get plenty of snow and time where the bike sits in the garage and waits. I always fill the tank with fresh gas, add a healthy dose of Sta-bil and ride it fifteen minutes or so to make sure it reaches the whole system. In the spring I run out the old gas and with the first fill up I add an appropriate amount of Seafoam fuel system treatment. I then take the bike out and flog its balls off. That stuff works wonders to clear any gunk out. Highly recommended.
I haven't tried the seafoam - although I've heard lots of good things on it from this forum - but I've actually been a fan of Techron for years. I run it through all my vehicles.