I've had the same problem with several PDF files, and I've found the way to fix them so the covers show up in iBook or other readers.
1) First you need to install Adobe Acrobat Pro (so you can edit the PDF files)
2) In Adobe Acrobat Pro, show all pages, and check if the first page is an image/cover, if the first page is not an image/cover, find the cover (hard drive/online) and add it to the first page and save the pdf.
3) If there is one image/cover, extract it to the hard drive, delete the first page containing the image/cover, save the pdf. Repeat step 2.