Thank you for documenting the issue. I have had this problem for a long
time.
I've now had a chance to try the encode with the same source and command
line on the official release 1.0.3 CLI binary for OSX and it does not have
the problem with the Closed Captioning track and mkv output, so that looks
like a smoking gun that this is a library version/packaging issue.
Package: handbrake-cli
Version: 1.0.3+ds1-1
Severity: important
When attempting to encode a video from a DVD image using a mkv output format
and also containing a Closed Captioning stream fails to mux properly and
produces errors. A subtitle track of the same type as stream 3 from the
following
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