Does your problem sound anything remotely like that guys problem? It's really weird that you can't see those fanspeed spikes in the logging screen of Afterburner. They should show up since I believe they are refreshed every 1000 milliseconds.
Actually nevermind I might have an idea what it is happening. I've had this happen in LFS when I vsynced it, since the game is really old (card runs it in low power mode and doesn't use more than 50% of the GPU then) the fan would spike up for a second and then back off to its default speed for a minute or two and then spike up again. Now if I removed vsync (fps were limited to 100fps) it actually stayed in 3D mode and wasn't switching and applied fanspeed in a more linear fashion.
But I see you already tried performance mode and other things, I was just wondering since some flashgames can actually get accelerated by the GPU, same like some Media Players (especially movie or video clips) can get accelerated and increase the temp of the GPU by 2-4C.