That's all I am getting from MLVFS. Empty Folders. Nothing inside them no matter what I seem to do or settings chosen.
Seems strange , I haven't had any problem with my 5d2 & dual ISO video with mlvfs .
Both PC & Mac versions of mlvfs work well but it
does take some time to process the 20bit image .
I use pc with
BarracudaGUI for cr2hdr dual iso , Very very Fast ! .
You have 2X2 chroma smoothing enabled , Vertical Stripes Fix (? why ,work with 5d3 not 5d2) , Fixed pattern noise (is it Noisy ??) , Etc.... ... processing time will take for every

.
Use just default values first (enable dual iso "full 20bit")and
try less files at once (maybe try just one) and all MLV file should be on the same drive as being extracted to.
Preferably on a SSD Or Raid "0" (minimum 2 spindle hard drives striped ) . I only turn on options only if needed !
Don't work of the CF Card copy the dual iso mlv's to your local drive and work from there .
Make sure your computer/Mac up to task of heavy processing (SSD , fast ram , etc.. )
If you want to be sure you recording is not corrupted , extract normally with mlvfs (disable Dual ISO 20bit) and
you should have a image that looks like it's interlaced.
Edit: just to be clear , did you refresh the web page after you selected your options ?