Unfortunately I deleted the problem files :( - I had a band video I needed to chop a section out of so I saved the two sections, one with a fade out and one with a fade in. I then dragged and dropped them both into Avidemux as I've done in the past - then tried to save the result using copy/copy but it keeps dying at about 1/3. I then used Ffmpeg's concatenate function on those same files and that worked fine. If it happens again I'll be sure to save the files.