Thanks for letting me know about that issue. I am actually just on the point of bringing out a new version of the program with a lot of improvements to the upload and download of spreads and pop-up notes. As soon as I bring it out (which may be as early as this weekend) I will post on the forum to let people know.
Quite a few things have been changed or rewritten in the new version as far as those operations go, so I would guess there is a good chance you will find the problem is fixed. If not I will try to fix it a.s.a.p.