It's because an IPad or iPhone sometimes has trouble opening a PDF file in a browser.
Download the files to your iPad / iPhone first and then use "open with iBooks."
We have tried this on iPads 1, 2 and 4 and it works OK on both with IOS 7 and IBooks.
If you aren't able to download the files to you iPad email us at email@example.com
and we'll send them as attachments. Then you may open them in iBooks and it should work fine.