I'm guessing it has to do with the Google Checkout button. For whatever reason that is in a table that wrapped itself around both left and right side column divs. Not sure how you managed that one
Take a look at your main.tpl page to see what's happening...
Also, you should check it out in FireFox with the FireBug Plug In installed. It will make your life so much easier to see what's going on.
Not to veer off topic , but what are the current rumors swirling around about an SP2 release date? I'm getting close to releasing a site and am debating on waiting...
I'd also like to agree that the standard sub totaling does look a bit strange...