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…
The differing lines and popping squares are not because of your color-blindness, someone did an absolutely terrible job resizing the logo images for the website and preparing the favicon. Also, rounded corners on the favicon? It's ok to give these jobs to an intern but someone still should check the results before pushing them live.
And what with being slightly colour blind, I've learned to suspect that it is probably my vision that is the problem.