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Actually, the cubes on the left and the unconventional layout give it a bit of a sense of depth - but have you considered making the static elements of the page change colour and keeping the main text area(s) uniformly coloured?

I think your colour scheme could do with some thought.. particularly this page: http://www.glasscubedesigns.com/default/02.html the red hates the blue... maybe use the adobe colour swatch for some inspiration: http://labs.adobe.com/technologies/kuler/

Ofcourse, you may want that ;)

Dropping the icons does bring it more in sync but it is now less obvious what that section is - it doesn't stand out any more. The vast majority of users will go straight to the left nav.

My personal portfolio website... I designed it to showcase a few pieces of work in an attempt to get into a university art course without any particular art credentials. I've deliberately tried to be experimental, but follow the conventions of good design in terms of typography and layout...