I have been having this problem with Frame 8 as well as in 9. When I generate my PDF, my bookmarks are not all where they should be. The will not always appear in the order of the pages, and they will be listed under other headings. An example would be, if I had 3 top level tags and each one had 5 things listed under them, When I generate, I might get 6 bookmarks under the first, 4 under the second, and 5 under the third, instead of five under each one.
I have done everything I can think of, and cannot come up with a reason why it is doing this? Any ideas? I can always send a section to someone so they can actually see what I am talking about. At this point, I am not 100% sure if it is Frame or Acrobat, but I am leaning towards Frame.
Thanks