So just as a follow up. I finally got the covers to go over for the 11 books I was fighting with. I am not sure what caused the problem and I did use Calibre to do it. Essentially I xploded the epubs in question. I then Deleted the covers from within. Redownloaded the covers. Reconverted the ebooks and transfered them over. Why it was not happening properly I can not say. Prehaps when i rebuilt the epubs I removed some corruption in them. Not sure and not sure what was different to make it work.
But my best to the Calibre team for such an awsome piece of software.. Kobo Dudes take some notes you need some of these features for the KDS.