Why are the wrong paragraphs included when I do a Save As PDF

I'm using FrameMaker 12 and Acrobat Pro XI. When I do a 'Save As PDF' from a book and select the bookmarks I want, and arrange their hierarchy etc. Acrobat includes paragraphs formats that I did not select. For example, it seems to include a random selection of TOC entries, which I DID NOT select to be included.

I've gone back and double-checked that all paragraphs have the correct formats, but it keeps happening.

Also, once I've generated the PDF, the PDF settings I chose don't seem to save correctly. In other words, every time I do a 'Save as PDF' I have to select the paragraphs formats I want to include as bookmarks again; it seems to have saved some of them, but not all of them.

Any ideas?