When you consider a computer with a 1920x1080 display is having almost 480MB/second of data read from it by FRAPS, it is a wonder the game can write to the video card at all.
60 times a second, there is 8MB of data being pulled from the video card. When that data is being copied from the video card, the game cannot write any data to the video card.
You could cut down the resolution, to reduce the amount of data, which should also help to smooth things out or as Imadot stated, reduce the frames/sec FRAPS is using.