You don't actually need to go through the long process of transcoding fmv files using ffmpeg. Instead there is a quick and easy fix.
Fix : Download the fps fix from here (drm free update ), extract it and paste the original or custom fps (40, 50,60 / i recommend original ) STFU2 exe of your choice( from the respective folder to the game's root folder (ie where the exe resides). Also download K-lite codecs pack, install it. Go to your start menu and type in default apps and click on video player then click on the klite logo (shows something else - don't remember). And be sure to lock the game at 30 fps using msi after burner / rivatuner or else it might crash while playing pre - rendered cutscenes.
Enjoy !