For me... personally, the logo doesn't work. I am slightly colour blind. The logo in the article I see just fine, and all of the squares are the same size. And I get it... Metro theme. The favicon.ico and small logo on Microsoft.com Those don't fair as well. The red and yellow squares are much larger than the green and blue, and my eyes see a throbbing line around the bottom and left of the red box, and a black line…
I'm part of that colour-blind chunk, and I don't see anything like what you're seeing. The squares appear to be an uneven size, but what would that have to do with our lack of ability to see colour? Colour-blindness comes in a great many varieties, and to be honest, if you're making something involving colour, you're going to displease some of them.
And I personally believe that this could (and should) have been worked around in some way since about 7-10% of the population has some kind of color blindness.