I'm extremly sorry about the delay in my answer, had to deal
with a family emergency and then I got backed up so that I couldn't
look into this until today.
I believe this is a duplicate to another issue, that's similar.
Permute internally uses a command line tool called FFmpeg (http://ffmpeg.org) and it also handles the
chapter writing. I've been browsing their bug reports and will see
that it gets fixed unless it's already been fixed.
Please, see if it fixes this issue. If not, I'll file a bug
report at FFmpeg and will post a link to you, so you can see the
progress. May I give them your contact information in case they
need to know some details about the file? If yes, which email
address may I provide?
Here's a debug log from the current public version of Permute
that I've been having the trouble with, 1.3.11 (571). The
conversion from Blu-ray rip with chapters in this case is the file
called "Serenity" in the log. (Sorry I left the others in there
— hope that isn't confusing.)
I will try a conversion of the same with the version 589 that
you posted, and let you know how that goes.
Unfortunately, build 589 doesn't seem to work. When I drag and
drop an mkv file on the window (or try to add it with "Add File to
Conversion Queue…"), the window's "1 of 1" and progress bar
flashes on screen for a split second, but then it does back to the
dashed outline and "Drop Media Here" without having added the file
to the queue. Please let me know what else I can try. Thanks!
If it doesn't help, please open Console (in the Utilities
folder) and see if any messages pop up while the file is being
dropped onto Permute. The messages don't necessarily have to say
anything about Permute itself. You can use Command-C to copy the