I know this is forum is pretty much dead (x2 years now) but I've had this same problem. I play MGS4 and it does it to me in an hour or so. Really bothersome.

Anyway, if this still is a problem, here's the pathway: increased focus on the screen --> less blinking --> eyes get unusually dry --> arteries on the surface get irritated and enlarge causeing red eyes.

For some people, having more background lights on helps (decreases fixation on the TV), but most important is to make sure you're keeping your eyes hydrated. Drops might help, but make sure you keep blinking. If you really wanted to go all out, you could probably invest in a humidifier or make sure you're really well hydrated while gaming (a little over the top, i know). Hope that helps.

http://www.eyecaresource.com/conditions/dry-eyes/

http://www.nlm.nih.gov/medlineplus/ency/article/003031.htm