I'm using the command line version of avidemux (avidemux_cli) and a bash script to convert my huge library of DVD VOB structure movies into mkv format. When using the GUI I open the first VOB file in the sequence and it asks to read in the rest and then it does the conversion. However, when using the command line version it still asks if I want to load all the other VOB files and so I'm required to be at the keyboard to type in "Y" and the whole point of doing everything in batch mode is undermined. How can I use the command line and specify that all the VOB files be used. For my case anyway, it sure looks like the default isn't such a good choice.
I just tried this on a second DVD and got the same result, so it's not an issue with the one DVD I tried when I made my first post. It looks like a real bug.
Have you tried to pass the --nogui option to avidemux_cli?