I would guess it's due to the /storage directory on the Vortexbox using an ext3 (or ext4) filesystem (i.e. a native Linux one), and the backup drive using an NTFS filesystem (i.e. a native Windows one). rsync will faithfully honour permissions when copying from one native Linux filesystem to another, but the NTFS filesystem permissions structures may not be a good enough match for the Linux ones to allow rsync to do the necessary in this case.
That's just a guess, and I can't easily test it since my system (including the backup drives I use) is pure Linux. But, if you're interested, you could test the theory by doing a manual rsync as root from a source directory on /storage (just make such a directory, and copy a few files into it) to a destination one on your backup drive; and vice versa. If you do take the time to do that, post back with the results so that we can all learn something
By the way, if you want to correct the permissions you've ended up with, you could easily do so using 'find', something like as follows:
Code:
cd /storage/music/flac
find . -type f -perm 755 -exec chmod 644 {} \;
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