Nothing's really wrong with the layout itself, it's mostly the colors, all of them are chalky, you have the chalky purple and the dull gray. If you could brighten them up a little, maybe do some little tricks with your headers, etc. Just make the menus pop out a little more, and it should show a huge improvement as far as the "standing out" problem goes.
I guess, all I'm trying to say is that the colors are a bit chalky, if you could make them stand out, in any method you can think of, it would most likely be for the better.