Mmm, that is odd. Have you tried doing a hard reset, this will wipe the reader and put it back to factory settings. Beware it will remove all books, bookmarks, collections so make sure you have them on the PC first. (you can't back up bookmarks though, although you can add them to the books in the eLibrary and it will add them when you transfer to book back in)
I find my reader can be iffy after I transfer books and it seems happier if after I transfer books I switch off via the menu after it reboots, then switch back on. Otherwise it seems to do odd things. It may be worth switching off via menu first then see if that helps. If not try the hard reset and reload your books, or maybe just the one PDF (sony user guide) to see if it reads it then.
Otherwise just hang on and Im sure there will be others along later with lots of help for you