When searching my site I get
WordPress database error: [Query was empty], it doesnt matter if result is empty or not. http://timmi.pointclark.net/
'wpdberror' prins before container div starts.
I have to refresh the index page several times to get rid of the error message, if that is a clue.
I never modified any core functions and only translated the relevant parts of search.php from Blix to Norwegian.
This may belong in the troubleshooting section, I'm not sure if it's theme related.