Can you pick one of the ones that doesn't have a thumbnail, right-click on it in a file list and do Library Tools->Update Tags from Library and see if it succeeds or fails?
Sorry I wiped the library and my hard drive before I could do this.
I have two issues going on here.
The first that I started with was the 3 tries to build cover art. I just used option 77 to reset MC and imported 130,000 audio files from my hard drive. I then built thumbnails. It took 3 tries. Each time it was finished I checked system info and it accurately stated the thumbnails. 64%, then 80% then 99%. I believe MC does the same thing on windows, just to a lesser degree. Maybe there's 700 thumbnails missed, not 40 percent.
Issue 2 was related to my previous post about repeatedly rebuilding thumbnails.
All the newly imported music on the Pi has image set to "Inside File". I did a Quick Find In File / Cover Art directory and it set all images to folder.jpg. I rebuilt thumbnails to get 100 percent first try.
This didn't stick after a restart.
Before I did option 77 as noted above I cleared thumbnails and all music from my library. I then re-imported and rebuilt thumbnails. Only 1 percent of thumbnails were built and MC basically didn't work. It couldn't display art or play music for more than a couple seconds. So it seems like the Pi doesn't like it when you import 130,000 files then a month later wipe the drive and copy a new 130,000 files, then a month later repeat. Is it running out of space on the 16GB card or are there too many temp files building up?
For now I have everything working well.