Out of curiousity, I used another tool to find files that had cover art embedded.
I used the same tool to strip the cover art out of those files and save the images to disk.
I see that some of the selections had two and three identical files embedded in the tag.
I imported the image files into MC, and for the same file from selections from the same album, some images are listed as type "jpeg", some as "jpg".
I have no idea on this because I always go to AMG and save their cover art image. It is always saved as folder.jpg. I then used MC to find the art.
Anyway, here's what I have done to try to figure out this recurring problem:
1- Stripped images from all audio files. No tool including MC shows embedded cover art now.
2- There were many Cover Art (Front) tags in APE and APL files. I have removed all these from all files.
3- Cleared the MC library with the reset option selected.
4- Emptied the MC thumbnails.
5- Deselected "save cover art inside tags when possible".
6- Imported again.
7- Rebuilt all smartlists and playlists.
8- Backup the library.
Every folder for every album has its art as folder.jpg and all those are jpg files.
For now, all is well. Every selection played has shown its cover and the library browser has correct art too.
So now the ball is in MCs court. If all stays well behaved, then I'll chalk it up to WMP deciding to tag files while using it to watch videos. I have disabled any file updates in WMP. However, WMP does not do APE/APL so that would not explain those tags.
No matter, with every file clean, every folder having proper art as folder.jpg if something changes I can say for sure what changed it and what the changes were.
More later!