Too cool yet to tell.
I had an '05 that only ever really bugged the hell out of me twice. Both times, it was 95F+ , stalled traffic , and less than a half tank. I remember being shocked at how much the tank was burning my thighs. At all other times, I found the '05 FJR heat very managable.
I've ridden the '06 in some 80 degree weather. So far, I haven't felt any heat coming off it.
Given the solution Yamaha borrowed from the "heat fix" farklers, and the success the farklers had with it, I'd say they've likely solved the "problem". On top of the Jiffy Pop, they've also increased airflow around the engine to eliminate the accumulation of heat.