IIRC Kovid said you need to check the box to enable sharing... under Mobi Output in order to get covers to show up (I could be wrong, but I read that somewhere). It didn't used to be that way, but something changed after an update not to long ago that made covers stop showing up like they used to.
If you want to read your PDF's without converting check out Mantano (or BlueFire or Aldiko or...) and you can read them that way. Mantano will let you highlight in multiple colors and add both typed and hand written notes.
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