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Anyone know where these are on the disc? I ripped all three full size files and none had them. In my blu-ray player, it appears to be a picture-in-picture track separate from the subtitles.

The most usual place would be in a smaller file as an extra. But some disk authors use subtitles for picture-in-picture effects.

I don't think it's hidden in the subtitle tracks because I can use english subtitles while watching the storyboards in PiP

Unfortunately, my Ponyo BD is in one of about 40 Banker Boxes, stacked around the basement. It's with my most of my other Ghibli stuff, but...

In a fortunate happenstance for you (maybe), it was in the easiest-to-get-to box. "Maybe" because mine is a Disney release, not the later GKids version, so there is a possibility it isn't the same.

I've set up the BD to rip every track over 30 seconds long, but I have to work in the morning, and MakeMKV says it's another hour plus to finish, so checking it will have to wait until then.

Thank you so much for checking! And mine also happens to be the Disney disc as well.

I have viewed every MKV file generated, and find none of them with an alternative video track.

I'm doing a backup instead, and will check that in a few hours. While that's running I'll also rip the DVD to see if maybe they put it on there.

OK, I'm not sure MakeMKV can do this...

A decrypted backup, playing BDMV/STREAM/00009.m2ts in VLC, shows two video tracks; One is the main movie at 1920x1080, the second is 720x482 and is the story boards. So it IS there on the BD, but none of the MKV files generated have two video tracks.

VLC puts up 2 windows when playing it.

Try it with MKVToolNIX GUI, maybe it can handle it and save the wanted into an mkv file.

mkvmerge can create a two-video-track MKV file, but there are still limitations. And 00009.m2ts is not the whole movie; it starts after Ponyo has been taken back to the lab; 00004.m2ts seems to be the first file of the movie.