I enjoy programming and working on my game for hours straight but my eyes just cant keep up. After about 2 hours I start misreading things and I cant focus my eyes without strain. After about 8 hours I no longer can even read the screen without being a matter of inches away from it. I have never had eye problems before I started programming. I think it may be the font but when I tried making it bigger it just made it harder for me to browse large numbers of lines of code.
Have you considered that it's not the size of the font that is the problem, but rather the color and contrast of both the font and the background?
Personally I can barely work with the default white background/black text that comes with most IDEs. In Eclipse, for example, I use the "Recogneyes" theme.
A dark background and low contrast ratio between the background's color and the font's colors can really ease the strain on the eyes.