After doing some research, I think I know what the problem is. IL-2 CoD (and apparently IL-2 1946) never technically ran in a proper full-screen mode. They run in a windowed mode that just fills the screen. This can confuse the card, as almost every single 3d game today runs in a full-screen mode.
Looking on
www.sukhoi.ru where Luthier posts a little more, he mentioned they are adding a proper full-screen option to the game. This could potentially fix up our issue. I'm not sure if it will be the Friday patch but lets hope so.
The clocks jumping up intermittently during the game is just from mouse activity. Watch the clocks when on the desktop while you move the mouse rapidly. They will jump up there as well.
As I said earlier overclocking in CCC will not work at all. The problem lies with the PowerPlay feature of the cards that dynamically changes the clockspeeds depending on what your PC is doing in order to save power and reduce heat. Overdrive in the CCC does not disable PowerPlay, so the clock issue will still exist.
Information for overclocking with MSI Afterburner for AMD cards can be found here:
http://forums.guru3d.com/showthread.php?t=338906
You only need to set the clocks 1Mhz higher for GPU and Memory to override the default clock settings.