Adding album art

I have a large CD collection that I ripped to FLAC. Adding album art was a real pain to do manually so I used WMP12 in windows 7. It found most of the album art OK but WMP12 does not store the album art in the tag. I recently had the WMP12 database get corrupted and I had to reload it. I only lost the DB not the files. They are extra safe on a RAID drive with regular backups. When I reloaded the WMP12 the album art was all gone. The jpeg images are however in the directory that contains the FLAC files. If I use MP3TAG to add the art and then save the files I dont lose the album art even if I reload the DB with that directory. The problem is that I have 18,000 FLAC files in several thousand albums and I dont want to tag the art manually even though the artwork is there. Is there any way of getting MP3TAG to do a mass pick up of the jpeg file in each album directory and then save the TAGs. Manually doing it is going to take me days.

Normally WMP saves the album art as hidden Folder.jpg-file in the album folder.
You can simply use the action
Import cover from file (String: Folder.jpg)