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I have something that might help. Concerning tables of contents in PDFs, I don't rely on the table of contents feature in my reader. Instead, I insert a table of contents at the beginning of my ebooks when appropriate.
I use StarOffice to make my PDFs. When formatting my ebooks I mark the chapter headings with a style (something like "Chapter Heading"). Then I use StarOffice's table of contents feature to insert a table of contents at the beginning of my ebook. It includes the page number where each chapter begins. When I want to go to a chapter I just go to the beginning of the ebook and punch in the page number for the chapter I want.
An advantage of this is that if I want to take my ebook to a reader with a different sized screen, all I have to do is reformat the ebook and then update the table to contents to reflect the correct page numbers. It also allows me to do multiple level entries in my table of contents (such as parts and then chapters within the parts).
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