When I got my new Nook Color, I copied over a bunch of (legitimately purchased but un-DRMd) ePubs. Only a few of them showed up with the correct book art, even with many of them showing the correct art in Calibre. Because of the publisher defaults regarding font and margin size and not being able to adjust them as completely as I'd like on the Nook Color, I have been using Calibre to explode the ePubs, rebuild them as .PRC files, and then use Calibre to convert them back to ePubs which keeps the formatting intact but allows me to adjust the settings I want (although there may be an easier way to do this). The point is, as part of the conversion back to ePub I have made sure I have the correct covers set in Calibre before conversion and doing this has made every one of the covers show up correctly on the Nook Color. I have also noticed though that if I upload more than about three or four ePubs to the Nook Color at a time, sometimes I have to cycle through the different sections of the library (magazines, extras) and change the view from thumbnails to the different lists before all of the covers refresh and show up correctly. My guess is that too many covers at once don't load properly because of cache or memory issues (I am completely making that up and guessing).