>
> Ah...does using FFmpeg on it's own mean the running the ffmpeg.exe file in the
>
> C:\Program Files\get_iplayer\FFmpeg\ffmpeg-0.8-win32-static\bin
>
> folder? 

Yes, run FFmpeg from the command line.
Open the "dos" window, Start -> run -> cmd
Then change directory (cd) to C:\Program 
Files\get_iplayer\FFmpeg\ffmpeg-0.8-win32-static\bin
Then try a command:-
ffmpeg -h
See if you get a response.

Then try to convert the file.
!!! The command I gave you before is wrong!!!
Don't use "-c copy".
Try a command like this instead:-
ffmpeg -i filename.partial.mp4 -vcodec copy -acodec copy filename.mp4

Maybe you will need to put the partial file into the 
FFmpeg\ffmpeg-0.8-win32-static\bin folder temporarily.

                                          
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