My guess is that FRAPS is a software therefore it is a process in windows and it is subject to alot of "interference". Maybe setting it to be high priority could help?
To that you need to add random system components (including PSU quality) that produce random differences every time and how much the game was optimised, particularly when talking crossfire. Maybe the "hardware capture" measures the frames at a very early stage before they are "broadcasted" to the screen and there is time until then for the whole thing to become unstable?
That said, AMD 7970 and 7950 owners KNOW that the random frametime review from that random biased website is overly exaggerated. I personally play Skyrim and have not a single issue. Oh well, maybe the release version had instabilities like those but not the recent versions! Playing the game with tons of HD addons and nearly 3GB vRam loaded and the game is perfectly smooth! Same goes for my smooth BF3 and Hitman recent experiences. On the other hand, FarCry 3 performance was bad, as described above, with frequent choppy frames and the effect of "bad frametimes" being obvious most of the time while the game is "AMD" special, as said above.