I suspect that Fraps itself is responsible for the stutters. I tried recording LEGO Rock Raiders videos and around 8-10 minutes, I get these annoying lag spikes. The intensity of the stutters are mild at first, but it goes away after a few seconds. Another few seconds gone by, the lag intensifies heavily. It was so bad, that I gave up on the recording. Defragmenting, cleaning up the registry, and purging junk files didn't do stuff to Fraps. I even have a lot of space on the hard drive.
If your version of Fraps is 3.5.99, try downgrading it to 3.5.9 to see different results. If it doesn't work, it's probably telling you to get a better hard drive.