I use calibre and convert the book to an ePub with output set at NOOKcolor and don't have any problems with book covers displaying. Unfortunately, sideloaded books won't show on the Home pages.

Admittedly, most of my books come from the Sony Reader Store and start out life as a well formatted ePubs. I deDRM all of them and convert them to look best on my sony Readers and my NC--two different conversions.

And the Home pages occasionaly display book covers that I specifically removed. For some strange reason they will suddenly reappear. There are definitely a few bugs to work out in the system.