Yes this happens sometimes. It is enormously frustrating especially with the Touch as you can't tell which book is which on the home screen.
For this reason I don't use the kepub version and never sync but prefer to download an epub into ADE which I can then modify (ie add a cover) in Calibre before loading onto my Kobo.
I read a thread just recently that suggested adding covers to kepubs may be possible in an update to Calibre soon.
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