Hello guys,
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.

If the PDFs in iBooks or other readers are not showing images, then follow the steps below:
1) Open pdf file in Adobe Acrobat Pro.
2) Save pdf file as Postscript file.
3) Open Postscript file and it saves as PDFs.

I have successfully fixed several PDFs using this steps.

What is strange is that iTunes shows all my covers properly! But iBooks fails 80% of the time. On my 800 .pdf books. Is there a good alternative to iBooks? This is a deal breaker. Just looking for a pdf viewer that has a bookshelf view that works, if that's not too much to ask, Apple, unless you deliberately cripple iBooks with pdf so I'll just re-buy all 800 books from Apple...

Anyway, GoodReader, and CloudReader don't show a bookshelf with cover icons. Kindle (at least the software version for iPad) seems to ignore .pdf files (coincidence?).

OK after all my whining its looking like Bookman solves my problem. I'll move all my books out of iBooks and use Bookman instead. Good move Apple. I'll remove iBooks while I'm about it.