After further review, I have more info on the 3 columns with "About Us", Twitter and Blog, that lose their alignment.

After viewing the source code for the page and comparing it to the code in tpl_index_default.php , I see that the first 2 DIV tags in the blog section are not being written to the page, and that breaks the page formatting, as the end tags are being written to the page.

Can anyone figure this out? Could this be related to the javascript calls not loading properly in the section above it?