Syahir: I ran into this tonight upgrading an old site. I upgraded from Wordpress 3.1 and I believe Graphene 1.3. When I had updated all plugins, themes and finally Wordpress (in that order) I found that the header was fine on the home page but when I clicked on another page the header shifted to the left and occupied about half of the header space.
I deleted the header and went to re-upload the image and I'm forced to crop any image to 60x198. The site is http://www.kimlingsacademy.com. I'm working in there right now but if you want access to the site to investigate I don't mind.
Thanks for all of your help. Craig