How would you do it? My current method is to use SMPlayer, seek to a matching frame in each video (very important that SMPlayer can frame step backwards!), and subtract the time (in milliseconds). This basically works, but it's not 100% reliable - sometimes it seems the relative timing is off by a frame, for unknown reasons. It's also a bit tedious, since I'm manually performing the subtraction and copying down the number(s).

The end goal is syncing audio/subtitles, so I'm not interested in video editors. I just want the magic numbers to feed to mkvmerge.