One small change I would like regards whatever magic runs the recent comments/posts widgets. I recently loaded the site on a work computer (!) that was sufficiently ancient as to not understand any of it, and the site loaded amazingly fast (excepting recent widgets, which were disabled). So I suspect that whatever magic runs it is blocking the site from rendering immediately, as it tends to take a couple seconds on my somewhat-modern-but-still-ancient laptop that runs Chrome.
Of course, I know next to nothing about dynamic webpages, so feel free to ignore this if it's completely misguided.
The main page should load without any of the widgets, but including javascript that triggers once the page is loaded to fetch them. I find your observation hard to explain.
What if the front page looked a little more like this?
(Please assume that I'm trying to help. If you're polite and constructive (even if you hate this design) Omega will send you bundles of love in the post. If you're rude, I'll personally fund ninja assassins to hunt you down.)