When you hit "Auto Encode" on the "Input" tab with no audio file selected, then check "Add additional content" on the "Automatic Encoding" dialogue and hit "Queue", there is an error launching the "Mux" dialogue. It pops up a message to say "Problem with audio input filename: The path is not of a legal form." Of course, at this point you have not selected any audio (since you are e.g. muxing original AC3 without encoding it).
You can just ignore the message, select sound/subtitles/chapters, and hit "Go". The output filename is disabled so you can't change it, but it loads the mux job in the queue with the default name.
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