Multiple issues

[serg]

If I "check" "Keep intermediate files" in Config -> General Settings and set Audio:passthrough all, "Hybrid" leaves temporary files with correct duration and create muxed output with wrong duration (See Debug).

However if I also "check" "No multiplexing and splitting" muxing not happens.
For now this is a workaround for me.
I tried to mux these elementary streams "outside" of "Hybrid"

ffmpeg -i video.avi -i audioac3 -c:v copy -c:a copy output.avi

Everything works just fine, muxed stream has correct duration

Then (after resetting "Hibrid") I tried to mux these elementary streams in "Hybrid" using audio:custom and encode to PCM.
"Hybbrid" creates 3 subjobs: 01_video, 02_muxing, 03_cleanUp. 02_muxing subjob takes ~10 times more than ffmpeg muxing (doing something)
and at the end nothing gets muxed, output stream consists only elementary video (See debug)

So, the problem looks like in the muxer(Mencoder) that "Hybrid" use for muxing (beside of unnecessary muxing call in "passthrough all" mode) and possibly in Audio encode procedure.