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It's a bit sad that although identical frames are being skipped, still audio has to be edited with this Blu-Ray. Normally if identical frames are skipped, no further editing is necessary. Can you double check with eac3to 3.27? Both 3.28 and 3.29 are relatively new and have a change in the code which might explain some different behaviour compared to 3.27. So it would be interesting to see how 3.27 behaves in comparison.
I'm not sure why different decoders produce different results in this situation. Sounds weird. If you can find a way which allows me to reproduce the problem on my PC, I would look into it. But without being able to reproduce the situation, there's probably not much I can do.
If you do "eac3to audio.dtsma audio.flac", does the resulting file match any of the three files you got from "eac3to bluray-folder 1) 3: audio.flac", using those 3 different decoders? Or is it a forth file, different again to the other 3 files?
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