vorbiscomment doesn't preserve file permission bits
I'm guessing that the utility actually creates a new file when tacking on the vorbis comment, which causes the permissions to be set like the default umask specifies.
There is another ticket, #136, describing the same problem, which was closed nearly five years ago. Apparently the bug has worked it's way back in. I'm on Ubuntu Linux 6.06, which provides vorbiscomment via the vorbis-tools package; this package is marked as version 1.1.1.