It may be the monitor you're using.
Years ago, when flat-screen monitors first came out, I had one that caused horrible eye-strain migraine headaches.
Working 12+ hours was almost a guaranteed migraine.
Take breaks and make sure not to stare at the monitor during these periods.
This helps for RSI issues too.
If possible, I'd try a different monitor (especially if the current one is older).
Make sure the refresh-rate is at least 60Hz at the resolution you wish to run.