jQuery in Posts

I’m using jQuery in my posts (added a jquery.js in my root directory and included it with <script type = “text/javascript” src = “http://www.syndrotech.com/jQuery.js”></script&gt;) and I ran into a problem.

It interferes with my theme’s menu. If you go to my main page (http://www.syndrotech.com) and go to a post that has a demo (i think all my demos use jQuery) them when you hover over programming or software nothing happens but if you go to one on say CSS without a demo the sub-categories come up.

Any ideas?
Thanks for helping,
Mark

PS: iFrames? Maybe?