I always get blinded by the first flash of lightning, but as long as I don't try to look at things while I sleep (the white text is not dimmed, thank goodness), I'm alright.
A lot of external factors may be involved: your monitor may be too big for comfort for this game, you may have been tired when playing or you may have some (minor) eye problem... I know I always had terrible headaches before I got my glasses. But it could definitely be a matter of focussing too much.
I suppose you tried setting your monitor brighter?
The game is supposed to be dark. It would be much too easy if you could see the enemies. The fact that you can only see their eyes makes it much more entertaining. That's why the lightning flashes can be very useful when they appear once in a while.