[spidergawd]

Ok, as I've said I don't use TLH and don't know for sure what's going on, but I'll tell you what it sounds like to me: the audio data of the files got altered somehow after the encoding but before the md5 was generated, and TLH is simply outputting the (no longer valid) checksums from the files' headers (metaflac outputs the MD5 signature from the STREAMINFO block). Possibly the files got truncated somewhere along the way before they were uploaded?

shntool's "hash" mode will output md5 signatures of just the decompressed audio portion of the files (as opposed to a wholefile signature), same as a flac fingerprint. They should match. If not, something has happened to either the audio portion or the fingerprint portion of the files. If you create an ffp file from the shntool hash output, it should verify in TLH. The question then would be WTF happened to the flacs?

Corrections appreciated.