When compressing with FLAC, some users receive a message like the following:
FLAC Message - WARNING: skipping unknown sub-chunk
The explanation on ETree:
Your .wav editing software (Sound Forge, Cool Edit, CD Wave, WaveLab, etc.) may have added extra unnecessary data in the header of the .wav file. If this is the case, the FLAC encoding DOS box warning will be displayed:
WARNING: skipping unknown sub-chunk 'LIST'
Don't worry about it... the FLAC encoder is just telling you that there's extra, unnecessary junk in your .wav file, and because FLAC is so cool, it's just skipping it.
And the explanation on FLAC's Sourceforge FAQ:
WAVE is a complicated standard; many kinds of data besides audio data can be put in it. Most likely what has happened is that the application that created the original WAVE file also added some extra information for it's own use, which FLAC does not store or recreate (see also). But the audio data in the two WAVE files will be identical. There are other tools to compare just the audio content of two WAVE files; ExactAudioCopy has such a feature.