Was a solution ever found for this problem? because I have exactly the same issue and I'm trying to make a ffp file so I can upload a show to the LMA. A side-issue is that when encoding, all tag entries are being filled with the file info, which is a new one since only a few days.
Tried restarting, and the computer's been switched off at various times the last few days too, uninstalled and reinstalled flac, etc. Is there any other way to extract the fingerprints?
Thanks