Você já tentou o VirtualDub? Contanto que você tenha os codecs instalados ou faça o download dos suplementos, a VDUB normalmente pode realizar a conversão.
link
De Vdub ( link )
And here's the first release for quicktime video (mov, some mp4,
etc.):
binary http://www.tateu.net/software/dl.php?f=qtvd_bin
source code http://www.tateu.net/software/dl.php?f=qtvd_src
"Quicktime.vdplugin" should go in your plugins32 folder and
"Quicktime.ini" should go in the VirtualDub root folder.
There are several different modes that can be used to open a movie,
these are specified in Quicktime.ini as "mode=." Mode=-1 and color=-1
are the recommended defaults but you can read about the different
modes in "Quicktime_ReadMe.txt." Eventually, these options will be
implemented as an "Ask for Extended Options Dialog."
Audio is currently not implemented and I am sure there are many bugs.
Questions, comments, suggestions, whatever...are welcome.
I will also most likely...someday...implement my avisynth OMF
importer.
E como executar os guias de conversão estão aqui:
( link )