I'm also having the same problem. All my sideloaded books are in my Pdoc Archive and they all show up on the fire with blank covers. But I was able to get the covers to show up by doing a factory reset. I also think deregistering and registering will work also. It also helps to have all your pdoc book download to the fire before deregistering. Very buggy this update.
Also a few of my Amazon books show up without covers too, so I doubt its Calibre.