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Are you using Win10?
The only reason I can think of that your DS Filter Settings change by itself is that Win10 updates change these filter settings back to the original Windows filters.
If using the Microsoft DTV-DVD Audio decoder gives you good results (check for Audio/Video sync problems) then of course you can use these filters. Or rerun the Filter Tweaker tool after each Windows update.
Ditching DirectShow altogether and using FFmpegSource as your source filters is an alternative. The only drawback is that the source files need to be indexed which can take some time for longer sources.
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