Somewhere along the line, we have lost the image size meta data from the database. The images and all various sizes still exist in the uploads directory. So when you reference the_post_thumbnail( 'thumbnail' ) it displays the fill size because it cannot find a reference in the database even though the file is there.
I tried running both Regenerate Thumbnails and the AJAX thumbnail rebuild hoping those might re-populate the size information into the database.
Any other ideas?