If you are using Windows 7, you may want to install your Fraps into a directory that is not under Program Files.
There is a new "security" feature in Windows that will prevent executable running out of the Program Files directory from interacting with eachother, but it only affects executables being executed from under the Program Files path. If you notice problems running TeamSpeak and or TrackIR too, then this is probably the cause.
I've been in the habit of installing all of my games in C:\Games\, rather than the normal C:\Program Files\ directory, so I didn't even run into that set of problems until I was researching a different set of issues with TrackIR.
Harry Voyager