Have you tried selecting the Acrobat PDF Preset PDF/X-4 ?
I just gave that a go - the same issue occurs with the text appearing too transparent.
I've just worked out an inelegant work-around:
1) export the book with compatibility for Acrobat 4
2) export the automatically generated Table of Contents document (which generates my bookamarks) with compatibility for Acrobat 5
3)inserting the ToC at the end of the PDF file
4) manually going through and relinking the bookmarks in the PDF
Far from perfect, so still looking for a solution, but I think my keyboard is safe for now at least...
maybe you can do both exports and "merge" the two files together in Acrobat Pro.
If I remember it right, you just have to open:
1. The export with the working bookmarks and:
2. Replace all pages with the ones from the other PDF where transparency is flattened.
The bookmarks should stay intact.
Did a quick test with Google Chrome browser and the Preview app on OSX.
Yes, I think this is the way to go. I came up with a much less user-friendly version of this literally a minute before this reply came though, but your version is much less work, which is always a good thing. Thanks!