Mine does it all the time. I can even make it do it, which seems a little odd. What seems to be happening is the cooling fan, comes on ALOT. I could be wrong, but there are times I am outside of my car, and can hear it clicking on and then off. Which concerns me a little bit for the future. Seems to be alot of work for the single small fan. And it seems that when it kicks on, it just drops the temp a few degrees below and then heats back up again.
As far as making the rpm bounce on my own, I can do it by just slightly turning the steering wheel, or give the brakes a slight tap.
In regards to the A/C running with the heat on. I just figured this out, but when you hit auto, it has the a/c engaged, hince the green light, but you can turn that off, by pressing the a/c button. That is what I always did, and it got annoying. Then I realized that by just turning the fan control will cause the climate system to run at the previous temp setting with no a/c.
Something else to consider. This may be going on for other non MS3, but our exhaust (i think) is rather throaty. And resonates throughout the cabin quite a bit. That could be why we notice it more. Just a thought.