As of version 0.6.47 (and still present in 0.6.48) the built in viewer no longer displays the cover in any Mobi or LIT files in my library. I have 2 books in ePub format that do display the cover in the viewer.
Loading a Mobi or LIT book just displays a blank screen at position 1, advancing past that seems to display the text of the book just fine. The covers appear just fine when editing metadata, they appear at the bottom of the screen when selecting a book, and they all appear in the cover browser. If you actually load the book in the viewer... no cover.