I would also recommend using today’s 2.4.10 BETA build. We have a new version of ffmpeg. Possibly may have fixed your ffmpeg profile issues and also a few fixes related to metadata matching.
If you’re still facing an issue please attach your conversion log with the 2.4.10 BETA run so I can see what’s going on. Also if you can upload the original file to the MCEBuddy server which has an issue with the MKV Unprocessed profile to our server then I can replicate the issue and deep dive into it otherwise it’ll be harder to pin down what’s going on.