Theres definitely something overheating thats slowing/cooling and then speeding up again for a few minutes.
I have that problem with my 6800GS now, since its generated a pipe fault that generates random green lines everywhere.
When in FEAR, it'll be running fine, and then slow down to a crawl and then speed up like yours.
I enabled the Nvidia temperature monitor, and to warn me when its exceeding core limits, and it reaches it at the same point it slows down, which is 117 degrees C...
The rest of my PC stays rather cool though, so its either your video card, or i guess it could be your CPU.
Everest might help you, as would the Nvidia tool.
It may be that your capturing the graphics card temp after it slows down, or while minimizing a game, etc, its cooled down quick.
If you do have the option to turn on Temp monitoring in that case, and for it to warn you, do so.
Press Del at bootup also (it should be that, or otherwise, it should mention while booting), and try and find within there something about CPU temps.
Ask it if you can (it depends on your BIOS version) to tell you to give a warning if it exceeds a safe temperature also. You'll know straight away, since it'll start beeping at you mid game.
I hope this helps