oh the eye strain and headaches. i get those too.
i think it's from over accomodating your eyes for way too long.
i usually get a headache and an achy pain behind my eyes when this happens.
things that help me are: wearing glasses instead of contacts, not looking at the computer as much, holding the book a little farther away, and every 30 minutes or so, taking a 30 second break to focus my eyes on something farther away. hope that helps. not studying helps too (but of course this is no option).