6
Since you said the site wasn't compromised, your theme file or css is messed up.
To be sure, do what MadFish said above. Clear everything in templates_c, except the index file (might want to refresh your view in your ftp app to be sure you got everything). Clear your browser's cache. Log in again, and if the theme is messed up, you know it's your coding. Hopefully you back up each file when you work on it?
Also, to repeat what was already said, turn off the "check templates for modifications" feature after you resolve your issue or are finished working on the site without the need to view changes.
I don't know.