Album Art Tagger worked just great.

After converting to FLAC, I added the FLAC files to a New MediaMonkey Library and ran the script. Success, the artwork is now in the FLAC files.

Thanks,

You could use this addon: http://www.mediamonkey.com/addons/brows ... rt-tagger/

To convert selected FLACs art from linked to embedded. (process 11)

No, Artwork is saved with the converted file as it was with the original. As WAV can't embed it will be an external Artwork.

Is there a way to convert WAV files to FLAC where the artwork is embedded in the FLAC file ?

When I try it, the FLAC files don't have the artwork. There is album cover folder.jpg in the new directory but no artwork in each of the individual FLAC files.
I've tried a bunch of ways to then add artwork to the FLAC files but too often I've either gotten nothing or the wrong art or wrecking other tags.

Is there some setting I am missing ? One that says include artwork in the individual FLAC files when converting ?