Never heard of F.Lux, I'll give it a try. Thanks for the tip!
I always use scanned line art so that also helps a little. The grey background also works wonders. It's not so bad now when I'm coloring during daytime but in the evening when our apartment starts to darken up, it can really turn into hell for my eyes. I'll see how it goes with F.Lux.
When it gets dark and your eyes start to hurt, you have several options.
1. Turn on some lights. 2. Lower your monitor's brightness and/or contrast. 3. Take a break, walk around the block, focus on something further away than two feet for awhile, maybe consider going to bed.
In fact #3 applies even to work done entirely in the day. Take a break every so often, stretch, get away from the computer for a bit.
Also yeah f.lux is awesome, it's on my computer, my phone, and my tablet.