i use mkvtoolnix but i have to do them individually. i don't want to re-encode etc just remux from flv or whatever to mkv. takes seconds but when there are 100s of files it's a chore.
can't see a way of doing it in the gui, just add file - add to job queue, clear and repeat
can't see a way of doing it in the gui, just add file - add to job queue, clear and repeat