I’d been having trouble with the wrong cover being used when compiling a MOBI file, and I finally figured out what was going on.
I’d deleted the document containing one cover, then I recreated it, and loaded a new cover into it (There is no way that I’ve found to just delete and image from a document).
I’d go to the meta data, choose no cover, then choose the cover again (the document was called “Cover”), but when I compiled, I’d find that the MOBI file used the old cover.
The problem: When selecting an image for the cover, Scrivener looks in the trash. I’d recommend excluding the trash when choosing a cover.