Michele, I think you can solve the layout problem (ziycon's screenshot) by clicking on 'restore template' or something similar within the admin panel. When you login there should be a message saying that template x,y,z has been modified. If you click on restore then those templates should align properly and the template changes should be kept as they are now.
I know it sounds a bit weird but It worked for me after my template was knocked out of snyc with the rest of the layout.