Atrotos: I took a quick look at your 2 games against that person.

Really, with the Fischer clock, you EACH have one hour of play. Your clock runs while the turn is on your page, and your opponent's clock runs when its on their turn. (Which you probably knew, except your post said "1 hour for the whole game")

The site checks for timeouts every few minutes (unless that has changed) so, perhaps he/she moved right before the site checked. I know I have seen plenty of games get to negative 5 minutes or more before timing out.