I stopped by because when I installed Firefox v3, I also got the colored boxes under the icons. I checked in the Performance section and 'use drop shadows' is checked, as it's always been. The system is clean., all scans updated and clean. I can change the color in Display> Desktop> Color, but there is NO option for no color.
I'll be watching the thread to see if any other suggestions come up. In my case, it is somehow related to FF3.