Testing with version 2217 and a few previous versions...
Select One-Click, pick a DVD .mkv file generated with makeMKV that had audio/video/subtitle date in the mkv container.
When the target is a .mkv file, when the "go!" button is selected, the audio is extracted from the .mkv file as .ac3 and the subtitles as .sub and .idx. Everything goes smoothly and it gets remuxed into a new .mkv file with the newly compressed h.264 video and nero AAC audio and subtitles.
When the target is a .mp4, when the "go!" button is selected, the audio is extracted, but no subtitle data is extracted. The original .mkv file is the same as used in the first example. The mp4 get's muxed back together and has no subtitle data. If I kept the intermediate files from the .mkv target, I can manually go and create a .mp4 with the subtitle data the .mp4 works file with the video/audio and subtitles.
Is this the expected behavior, in that mp4 files will not be muxed together with subtitle data, so no subtitle data is extracted? I tried installing a new version of mp4box into the megui tools directory, but that would only help when muxing the streams back together.
Thanks for the clarification on what the expected process should be.
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