Hi to all...
I've been facing this issue both as an editor (http://revistas.csic.es
) and as a reader with iPhone4 and iPad2.
Just by chance a while ago I found that at AJOL (African Journals Online) behavior is quite different.
For instance, when I go to the PDF link here (using Safari/iPad2):http://www.ajol.info/index.php/ajrh/issue/view/8254
PDF opens in a new page in full and becomes downloadable to iBooks for instance.
Maybe opening the PDF within a frame is the problem...?
Hope this can help. Cheers,