Oh and here is an odd update: I opened one of the two PDFs that are currently on my iPad on my iPhone by using Dropbox (this was the source from which the PDF made it onto the iPad in the first place). After opening the file on the iPhone, I touched "open in..." and chose iBooks. The file opened in iBooks, which filed it into the same collection in which I had placed it on the iPad, and my bookmarks were synced. Bizarre. Another example of how Dropbox is far superior to iCloud, even when trying to do things the Apple Way.