If you have the option checked, every time MC saves cover art, it should write it into the FLAC file. As long as you have WRITE permission on that file, MC should succeed. If it does not succeed, it should give an error message.
The relevant option is: Tools > Options > Files Location > Cover Art > Also store image in the file's tag > (checked)
I'm also using the "in same folder as the file" option, which means I have one .JPG file named with the Artist and Album in the same folder as the songs for each album.
How do you know the cover art isn't stored in the FLAC files?
Brian.