I am using an MU install. When I go to edit my theme in the main MU Dashboard, I am getting messed up code showing in all the files except the CSS.
Below is an example of what the footer.php looks like. They all look pretty much like this. I am using the Love The Orange theme, which isn't specifically causing the problem. Something else is.
http://i284.photobucket.com/albums/ll29/awdevore/bad_footer.png