It *is* some kind of window sizing issue, but I can't seem to fix it... if I import a file into the library, for example, most of the text with the file name, description etc. is off the left edge of the window... but there doesn't seem to be any way to resize it -- if I move to the left edge of the screen, all it lets me do is resize the main window, it doesn't let me bring the missing left pane back.
As far as the PDF issue, there were a couple of files I tried to copy over with Calibre, and when I opened them up on the PRS-300 all the pages were blank. Then I tried it with the Reader software on another machine and the PDFs displayed properly. So don't know if it was something unique to those files or just a one-time glitch or what, maybe I'll try it again. Otherwise I'd agree that Calibre is the way to go.