The new look CYS that will eventually come out will probably fix this. In the meantime, try f.lux. It looks a little weird at first but you get used to it. Basically, it makes your computer screen sepia-ish at night time (which apparently helps a lot with sleep, too). I've been using it for about three weeks and I don't get tired eyes at night anymore.
Alternatively, if you're on a Mac press control+option+command+8 to invert the colours on your screen (white becomes black, black becomes white, CYS banner becomes blue etc.), and if you're on Windows just search the internet for a program that does the same.
