I don't know if this will help, but I mentioned in my workflow video how I had to use MP4Box to correct an issue with the MP4 file that XSplit produces. If anyone is interested in using this, then feel free. Basically all you have to do is unzip the 3 files into a folder and then drag and drop your MP4 file onto the fixme.bat file. It will demux and remux the video and audio into a "fixed" file.
http://shows.anairo.com/convert.zip
I cannot offer any support on the workings of MP4Box.

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