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it basically lists everything in the source dir followed by everything in the destination dir, ie:

/media/video/original_series
./TEST2/TortillaFlaps.s01e05.mkv
./TEST2/WestOfPesos.s01e08.mkv...

Jim, Thanks for you help.

It nearly works - the new directories are created but only the last mkv file in the last directory is transcoded, for example if I have:
dir1 - file1.mkv & file2.mkv ...

I have a batch of mkv video files I would like to transcode to a more compressed format. After spending a significant amount of time experimenting with various parameters I think I have found the...