This sounds to me like it could be a file encoding issue. I would recommend checking to make sure all of the php files that make up the theme as well as all Wordpress core files that might have been modified are UTF-8. You can do that in your code editor, or by checking each file here: http://people.w3.org/rishida/utils/bomtester/
A quicker way to narrow down the scope of potentially problematic files might be to create a clean dummy Wordpress installation and activate the seemingly problematic theme. If the problem is still there, it's got to be a problem with one of your theme files. If it's not there, I suspect that there might have been some unsound edits made to the Wordpress core files.