you have to run the game then manage to have enough resources to act as an audio/video buffer while fraps waits for hard drive time (which it would get plenty of if there wasnt a whole lot of swapping going on). when your resources get low you kinda have to dip into the swapfile for virtual memory, and fraps doesnt write its buffers to disk as fast as it wants to, so it tries to allocate more memory for buffer, you run out and it goes for the swap file. performance is lost and it cant keep up with the stream of data coming it.
you could try disabling mediavps and free up some ram, that might let you record without as many gaps.