As far as I understand things, there are 4 ways to store cover art in MC (BTW you might want to update to the latest version), 1. in the MC cover art folder, 2. as folder.jpg in the album folder, 3. as Artist-Album.jpg, and in the Tag. You can also save image in tag and one of the first two.
MC uses ID3 v2. I have all my cover art stored in the tags and as Artist-Album.jpg in file (album) folder and virtually all my cover art is present, so you should in the end be able to find and show all you cover art.
One the advanced guys will be along and be able to help you, so welcome to the most powerful media center on the planet and the forum, answers come pretty quick most of the time.