They either resized a bitmap image or they rasterized a vector image that wasn't properly aligned, thus some of the squares have some of the borders antialiased and the space between squares appears to be wider between some than others. Also, they are different colors with different lightness levels and that has additional impact on the appearance of different width of the empty space.
This has nothing to do with color-blindness, I can see it, too (I was non-color-blind enough for my driver's licence.)
Actually I just tried to "fix" the favicon in Photoshop and even if I aliase the edges manually it still doesn't look right because of the different brightness levels.
And what with being slightly colour blind, I've learned to suspect that it is probably my vision that is the problem.