Fraps hooks onto the 3D Portions of the program, so if you have it full screen, you have to use your keybinding while in game full screen, and not go out of it. That said, if you have multiple 3D Applications running (I suggest turning off Windows Aero) don't give focus to other 3D Applications, I know fraps hooks onto the first it can hook onto, but I've had it sometimes get confused and hook onto another program if I focused it.

if nothing helps, then it's a problem on your end, fraps team will not reply to something like this sadly.