Make sure you're setting the software to record at a framerate that fits the speed of your computer - or drop the detail settings in FS to make it easier to record video.
I play both FS2004 and FSX, and with FSX, even a 6 core CPU, 8GB of RAM and two Radeon HD 5870's are not enough to play the game at full settings, nevermind trying to capture with FRAPS.
I usually capture my videos with a 30 FPS setting on Fraps too.