Fraps does not register CC as a game is their a way to change that?

Yes. Don't use Fraps.

Holding down printscreen spits out every frame as an individual image to the Cortex Command directory. Then you animate them into a .GIF.

Or you can use AnimGet. It was originally designed to record other games, but it will work for CC.

http://www.gmdsoft.de/menne/z3c/animget.htm

Press 2 during the game to slow down time so the program can capture all the frames. (1 speeds time up)

Once, I was able to record CC B17 with fraps. Make sure the window is maximized. I can't remember the settings, I just fooled around with them. But the quality was kind of bad, and IMO, it can't beat using Print Screen and a gif animator. AnimGet would be a better alternative to fraps, just make sure to slow down the game. Prnt Scrn > AnimGet > Fraps.

thanks, and do I compile them in gif animator?

or you could use the search buttom, Simillar topic was here some months ago.

You could use Camstudio.
Just put it on windowed if you play in windowed or fullscreen if you... well you know.

whenever i try to record something using camStudio it always goes really jerky, is there any way of easily recording a video with the game running at full speed?

i am trying to record a walkthough of marathon BTW