On Mon, 21 Jun 2010, Paul Rubin wrote:
First off, make sure you're not in handout mode, which nukes the in-slide navigation links (but leaves any section links in the header/footer/sidebar alive).
Paul, I've never used the handout mode and the .pdf is created from within LyX using pdflatex.
Beyond that, you might try changing the theme you're using just to see if they come back. (I'm wondering if it's polar bear in a snow storm time.)
I looked at another old .pdf using a different theme and the links are visible and working there. The presentation with the problem has always had a white background, but the links were still visible and usable. Now I just need to relearn where the theme is specified and change it to one that works. :-) I tend to copy the filenames then create a new presentation from an existing one. Saves me a lot of time and effort. Thanks, Rich