i believe the shntool md5 is the same calculation as flac fingerprints. they look at the audio content.
the old md5 checksum files that came with shn sets, are wholefile md5 checksums.
http://www.thetradersden.org/forums/...ad.php?t=17951
all shn sets above also come with md5 files. i've checked them all, and they were all fine. (i didn't share those md5 files, as i thought they were of no use.)