Thanks to the library Dom sent me, I was able to track down the problem. It looks like if you crop a lot out of a page (40+%), it causes major clipping issues where annotations stop getting drawn both in the annotation editor and in the normal song view. The fix should be pretty easy, but I'm going to be out of town for a couple days so I won't be able to get the next update together until next weekend. The only workaround on Windows at the moment is to get rid of the cropping (or crop less).
Mike
Mike