Got a problem with sidebars and footer after upgrade.

Just moved a site to the hosting which support new wordpress . Naturally I decided to upgrade. I know that new WP doesn’t “work” with old theme and the other way around (I’m running ahatualpa on the other site for some time). So I decided to switch to default theme and then upgrade. My admin panel didn’t hit white screen but I end up with site which doesn’t show right sidebars!!! Somehow this default theme change something somewhere. Worth, I deleted theme (from admin panel) and installed it again. And still the same picture!!!
Please, help! I don’t even know where to look.