infinate jQuery vs HTML Link

infinate jQuery vs HTML Link

I have a page that has animation that repeats infinately. This is implemented via a jQuery script that calls itself. The page also contains a menu implemented via an unordered list with href links. The menu works ok on a test page without the script. When I add the script the menu no longer works. I am not sure I understand the event model and potential conflicts between jQuery and HTML events. I would appreciate help with my specific issue and perhaps a nudge in the direction of some documentation on the event models in general.