This is driving me nuts. I'm testing a bit around with videotranscoding and try to convert a 28Gb .mkv to a smaller .mp4 file. The .mkv File has 39 Chapters (2,5 hours), but whatever I'm choosing within handbrake, it only encodes the first one (6:23 Minutes).
I tried different profiles and custom settings, but the result is always the same. The .mkv File was created with makemkv and can be played without any problem with totem in full length.