Comments.php disables javascript in header?

Odd problem. Whenever one of my pages calls for comment.php (e.g. single post pages and one of my pages called “Ask Me” that allows comments), a javascript that I use for a cool sliding doors feature in my header stops working. This annoys me.

My comments.php was copied and pasted from the Kubrick theme so I could allow for the new threaded comments feature. Everything else seems to be working ok.

Any ideas?

(site is summertomato.com — to get past the Maintenance Mode screen use ID: friends Pass: access)