flac is rather sensitive when it comes to include images files into the encoded file. Other than mp3, if a image file format is not correct it would not include it in the resulting encoded file.

You can avoid this using my Exact Audio Helper for Exact Audio Copy v1.5 and Audacity Audio Helper to create your library, as the scripts contain a working step where image files are converted to compatible format with the help of ImageMagick.

To find those files in an older library, or one where ImageMagick was not used for image file conversion, here are the commands to be issued on a linux host to find the directories with missing flac files

find <parent dir> -type f -iname '*.flac' -printf '%h\n'|sort|uniq > flac.txt   # this command finds all directories which contain flac files (replace "uniq" with "uniq -c" to have each line preceded with the count of files found)
find <parent dir> -type f -iname '*.jpg' -printf '%h\n'|sort|uniq > jpg.txt     # this command finds all directories which contain jpg files (replace "uniq" with "uniq -c" to have each line preceded with the count of files found)
grep -f flac.txt jpg.txt # find common lines in both files
diff flac.txt jpg.txt # find line differences in both files