I'm new to this forums and have little expertise with eReaders. However, I have noticed this exact same problem that Jack is having (covers disappearing).
Calibre definitely places files on the kobo eReader. Using Calibre to push books I have had similar problems and become quite frustrated.
There is something I noticed about this but not sure if it's relavant or not; When Calibre transfers books to the Kobo it automatically creates sub-folders according to author by default. I have found that if I remove the .epub files from the sub-folders and place them in the main directory of the kobo everything seems to work fine (the covers come back). Also so far I have yet to have a storage error on this particular reset although I am just waiting for it to happen.