Just another update, after doing some research, I've been using Sigil to open each ePub and then save it without changing anything. I then go into Calibre and manually select the cover art from within the directory Calibre has downloaded it to. I then convert the ePub to ePub. Doing this has had EVERY SINGLE book cover show up correctly (and this number is in the hundreds). If I don't do either one of these two things, the cover doesn't show up, so I'm not sure what is ultimately responsible.
On a side note, I'm using a Mac and on occasion have forgotten to 'eject' the Nook Color before unplug it. I've had a number of issues with the library having to be rebuilt and the books disappearing and then having to be rescanned before showing up again. On one of these occasions a large section of the books suddenly had their cover art disappear. After deleting these files from the Nook Color and then transferring them again (without changing the ePubs at all) the covers were suddenly back. This again leads me to believe the Nook Color software and not the ePubs themselves is what is causing the issues.