I just remuxed some stuff with 4.1 and I'm not seeing an audio mute problem. Everything seems fine for me. I'm simply adding PGS subs from a file back into my MKV's so it's taking an existing one, adding PGS subs to it, and writing it back out. No problems.
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HTPC: Windows 11, AMD 5900X, RTX 3080, Pioneer Elite VSX-LX303, LG G2 77" OLED
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