The javascript would most likely be in your default text box, which is at the very bottom of the Global Preferences page. This is where you would have inserted the PayPal logo, and any other text that you wanted to appear in all of your auction descriptions.
Deleting the default text only applies to new auctions. It won't change anything in auctions already launched. You would need to use the revise auction form on eBay if you needed to edit those auctions.
