There is also an extensive discussion that might be of interest here:
Of course, you do not have that problem with your TX1 as it uses the usual MJJPEG encoding.
'HandBrake' worked well but the developers tell me that AVI support has already been removed from their current development software.
For non-stereo movies you can certainly buy commercial editing software.
However, for twin-camera stereo it is normally necessary to use 'StereoMovie Maker' for its auto-correcting of distortion and alignment.
For that reason, the Canon MOV files have to be converted to AVI.
SMM will read 'older' MOV files.
If someone is really clever maybe they could add support to open-source 'HandBrake' for other AVI codecs ?