I have a Gel Seat too, and have the same issue if it sits in the sun. I have to park the bike somewhere that will have been in the shade for a few hours before I leave the office. I am trying to decide whether to go with a new seat, or just buy something reflective to put on the seat when not in use. Seems that sun is what gets it really hot.
Red 2006 V-Strom 650: "the most shockingly competent machine in the world today"
Alpenkönig (a.k.a. King of the Alps): 2005, 2006
1989 Sportster Bobber Hardtail
1990 Electra Glide with Cop Bags