thanks for the reply 44vince44 - yeah I had manually deleted all files in the temp processing folder, same thing every time. One trick I've found which most of the time works is use mkvtoolnix gui and just process the file to a temp directory, if there any issues with headers etc. that usually seems to fix it.
I might try splitting the audio and video and then remuxing them - file plays fine but obviously there is an error in every episode from the original ripping.
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