The Fraps codec (FPS1) is put on the system when you install Fraps. If you’ve reinstalled Windows you will also need to reinstall Fraps in order to play back your movies. Please keep in mind that if you want to give your raw footage to another person they will also need to have Fraps installed.
Your media player may be having trouble keeping up with the large amount of data Fraps has written to disk. Fraps is optimised for processing large amounts of data, but many players are not. If they can’t read the data fast enough skips in the video and audio may be present.