Are you using the most recent version of mobi_unpack? There was a bugfix (relatively) recently that had to do with missing cover images, is why I ask. At least I
think I remember that being a mobi_unpack issue. Could have been something else, though .. my brain's pretty tired lately.
I just checked: "Fix for cover metadata" in v0.52 ... current version is 0.54. So if yours is earlier than 0.52 ... that's probably what's up.
Mobi_Unpack download post.