Some more information on the borders disappearing issue. First thanks to everyone that shared what they did to fix the problem when they had it. None of these fixes seem applicable to us. We don't have graphics bleeding over on the slides or smart shapes near the borders that are disappearing.
We've published the projects in Flash 9-11 and the borders are still missing on the bottom and right sides. When the project first starts the title slide had the borders but the slides following don't have the borders. When you go back to the title slide the borders are no longer there either. This is very frustrating.