Well don't think there's anything wrong with your fraps settings at least, if the raw footage is flawless.
Was this the only video you rendered or did you do more which were lagging as well? If this was your first time, try again to make sure it wasn't just something that went wrong with the process. Or you can try different codec shall it perform better. I always used the famous thiras' two-pass method (
here) which worked great for me. It's a little harder to execute but should give you wonderful results if done right.
...And make sure when rendering to not to do anything else stressing with the computer. At least that's what I was told anyway
.