[Five]

diggrd is right... CEP/Audition puts 'unknown sub chunks' in the header data on every file it saves. If its a cue sheet or something I need I'll save as APE, however to get the cue sheet back in CEP I have to first decompress the WAV before I load it in but that's another story.

Anyhow, don't worry whatsoever about 'unknown sub chunks' only worry about the audio content!

If you want to verify that the WAV and FLAC files are exactly identical audio content, generate an "st5" checksum from each and the hashes will be the same (see tutorial in my signature "checksums demystified").

The next thing you've got to check for and repair if necessary are SBEs or sector boundary errors. Run a "len check" on the resulting FLAC files .. this is important (see same tutorial)..