Try Tubedigger,
Hit the "convert" button, and check "Fix FlV2", load the file and hit the "Fix Flv2" button.
The fixed file will be in the same folder as the original and it will say "fixed"
It's what i use on MFC files. Let me know how it works for you.
Tubedigger:
http://www.tubedigger.com/TubeDigger_Install.exe