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It works fine for me, both with "Sync Books" and "Don't Sync Books".
Comment: "Sync Books" has nothing to do with syncing metadata. Instead it copies the book file if the version in the calibre library is newer than the version in CC.
Question: are you using a plugin that "manages" the last_modified date or are you changing it yourself? CC and calibre use that date to determine if calibre must send new metadata to CC. If something is changing that date then there is a good chance that CC won't be updated.
The test: Display the last_modified date in the calibre spreadsheet. For some book, make a note of that date. Use "edit metadata" to change the comment for that book. Check that the last_modified date has been changed to now. If it has then in CC connect as a wireless device, not syncing books. Let it sync, then disconnect. Check that the change you made to the comment is now in CC.
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