That’s a theme issue and has nothing to do with a core upgrade. Unless you provide a link to a page demonstrating the problem, no one will be able to offer much in the way of assistance.
Here is the link to my site: http://www.thedoctorweighsin.com
Look at the difference in how it appears on chrome vs ie (or Safari). In the latter two, not only is the nav bar messed up, but the current posts are not showing up nor is the Share plug in.
I don’t know what you mean when you say this is a Theme issue
Try switching to the Twenty Eleven theme and you’ll see what I mean. Your theme controls most of your site’s display/output. Right now , you have 58 validation issues on your Home page alone.
http://codex.wordpress.org/Validating_a_Website
The developer at my server company found that the autoinstall had disabled a critical feature. He re-enabled it and it fixed the problem. So it wasn’t the theme after all. It is something that doesn’t work well in the auto-install
I also found that is disabled plug ins, like Askimet and my Share button. It said they were re-enabled, but they weren’t – I found out when got spam and complaints from readers.