Curly, thanks for that link. What a bizarre problem, but that is exactly what happened to me. I downloaded PDFs first, and they worked fine. Then a couple of days later I downloaded both PDF and epub files, and the epub books worked but not the PDF. I just assumed the PDFs I downloaded earlier would still work, but I just checked now and they do not. So I can only read the epub files on my reader right now, not the PDFs.
Also, thanks netseeker for your post, it is good to know that there can be random problems like that.