I recall seeing another post about this issue and I can't find it now, but none of the workarounds mentioned there worked for me, so here goes:
I am working on a book migrated from FM 9 to FM 11, and when I print to PDF, I specify the bookmarks I want to display in the Bookmarks tab of the PDF Setup for Selected Files dialog. The PDF prints fine, but when I want to print the book again, FM doesn't remember my settings, forcing me to set the bookmarks from scratch every time. This has proven pretty tedious seeing that I'm working with an old book in which the styles aren't intiutive, so trying to remember all of them every time isn't the best of fun. When I print a single file in the book, the settings are saved properly.
In the previous post, I remember reading that this was a bug in FM and trying the following suggested workarounds (none of which worked): Switching to structured mode; saving the desired setting in one file in the book, printing that document, and then printing the book (was supposed to result in FM remembering the settings for the entire book); saving the book right after it prints; selecting all files in the book and saving as PDF, as opposed to selecting the book and then File> Save as PDF.
I'd be glad to know if anyone has any ideas, or if Adobe are planning to post a fix for this issue.