It's a Cowon S9, so it's either MSC or MTP (I forget which mode it's in right now). It shows up via drive letter if that helps narrow it down.
I don't use embedded album art, so the files not syncing are saved as folder.png and folder.gif
I didn't even think to check the album art in musicbee but it looks like the album art doesn't link to the files unless I do it manually. When I do, it shows up in musicbee just fine.