Почему FFMPEG сообщает о неправильной продолжительности?

You can try tcprobe, part of transcode pack.

I'd guess it's a problem with the file. The length is probably written in a header incorrectly. Unfortunately there is no such thing as a validator (like for web standards) so you can't know for sure if a file is correct.

Check it with a newer version of ffmpeg (you don't have to replace your build), and if it gives the same duration you can probably blame the file.