How to make pdf annotations show up on iBook?

Hi. Here's what's been going on:

I take lecture notes on my computer by downloading the lecture powerpoint beforehand as a pdf and annotating the pdf with my own notes. Then, so I can have my notes on the go, I sync the pdf to my iPad iBook app. However, my annotations do not show up on the iBook version, although I am absolutely certain I am adding the correct file to my Itunes library. On my computer, the exact same file DOES show my previously written notes. I have tried duplicating the file and adding that one instead, resyncing, etc., but nothing seems to work. Any thoughts? Is there a setting I need to tweak