I am not sure if this is related, but I had a problem where the text was fine, but the iPad only didn't show illustrations in the PDF file. I opened the PDF on the PC in Acrobat X and saved it a "Reduced size PDF" using Acrobat 5 compatibility. I think the illustrations were included in the PDF file as "attachments" and perhaps Acrobat 5 format doesn't support that, so the images were incorporated into the file differently on Save. This is just a guess. (I also tried saving with Acrobat 6 compatibility, but that didn't fix the problem.)
My primary use for the iPad is viewing mostly technical PDF documents and this is proving a bit unreliable because some of the documents are protected from changes so this fix will not be possible on those.