Version 1.4.1, Ubuntu Intrepid, x86. Tried to make MKVs from a DVD with 4 main titles, selected one audio track and three subtitle tracks on each.
Thanks for the detailed report.
Bug one: I cannot use "~" for my home directory when selecting the output folder. MakeMKV will just prepend the folder the binary package was compiled in, so "~/stuff/video" will become e.g. "/home/someuser/compile/makemkv_v1.4.1_beta_bin/~/stuff/video".
This is strange - I personally haven't seen that. We'll investigate.
Bug two: when the extraction process is aborted, MakeMKV goes back to the display of the disc's structure (tree with titles, audio tracks etc), but some titles will be missing. The only way to get them back is to start over by selecting "Close" from the "File" menu (but see next bug) or closing and re-starting the application.
This is likely to stay this way for a while. When you abort the conversion the "title" stays in "half-converted" way. That's why it is hidden.
Bug three: "Close" from the "File" menu often does nothing.
Very strange. Noted.
Problem with saved MKV files: I have yet to find a player that the plays them properly. In VLC, there is no sound, even though VLC sees the audio track and selects it by default. In Mplayer, subtitle rendering is garbled (only with overlay video though, so this might be an Mplayer problem). In Kaffeine, the first 30 seconds are skipped, only one subtitle track is available (out of the three I saved), and there are A/V synch problems.
Obivous question, but did you select "stereo" output device in VLC (or if you have SPDIF output, did you enable it in alsa mixer)?