Programs like FRAPS wont pick up on Frame-rating issues. They record the FPS being asked for by the game engine, not what is ultimately displayed on the screen which is what frame-rating is about.
To properly benchmark frame-rating performance, you need a fairly beefy capture card writing to a large SSD RAID0 array. Applications are starting to come out that an estimate frame-rating performance, but you need the above setup to do it properly.
are you sure because i thought FRAPS shows you how many frames per second your getting? it can ask for whatever but the better hardware the higher the fps but not sure if it takes microstuttering and latency into account. not sure i understood but i think what your saying is no it dont take into account latency and microstuttering so dosnt therefor show the proper fps?
FRAPS and programs like it show you how many FPS are being demanded by the game engine, which changes dynamically based on the resources available. To an extent it also measures what is provided, but recently the discovery of "runt" frames has messed that up a fair bit.
Frame-rating is fairly complex thing to understand
Skip to 0:30:00 on this video, where there is a quick explanation of what Framerating is. http://www.youtube.com/watch?v=noVu8BXkCsw
Everything after that is worth listening too, the interview goes for about half an hour.