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However, instead of making a normal MKV I found that the Backup function actually worked fine (before opening the disc to select titles, choose Backup from the menu instead). I did try to process the resulting backup files into an MKV but the above issue occurred again. The backup files play normal...

I've been ripping a number of my Blu-Ray discs (around 80 now), and this one is the first to have given me any trouble. MakeMKV has otherwise been a pleasure to use. :) It's disc 1 of the Vision of Escaflowne on Blu-Ray (the UK edition). It is brand new and absolutely spotless. The disc seems to be ...