Rated 4 out of 5 stars

I have focus issues as well, even on a new profile with only Autopager installed. Whenever a new page loads (like loading 3 pages immediately on Google for instance) the search box loses focus. It is a bit frustration to re-get the focus and resume typing just to realize that focus was stolen again due to the third page loading. I'm a bit surprised it was not reported before, as I have been having this issue for quite some time, and finally decided to report it today. (To my surprise, someone beat me to it by a few days though.)
But Autopager is still great and a real time saver.

This review is for a previous version of the add-on (0.5.5). 

Could you please make sure you have last version of AutoPager and Firefox?
Could you please check whether you have CustomizeGoogle installed? If you have, please uncheck "Give the search box focus" in the option of it.

AutoPager load next page in a hidden frame. If the page set focus in the load event or if you have any addons which set focus on page load then the focus may be set to the hidden frame autopager used to load the next pages.
Regards
Wind