Multiple Javascript Issues

I’ve been having some problems that I believe are connected to calling multiple JQuery files in the header, but I don’t quite understand them and could use some help parsing it all out.

<?php wp_head(); ?> appears to call JQuery 1.6.1 properly. Even so, I cannot use JQuery on my site with this alone. I added <script src="//ajax.googleapis.com/ajax/libs/jquery/1.6.1/jquery.min.js"></script> and it works perfectly. As long as I have that call to the googleapi version in my header, most things go smoothly.

Of course, something strikes me as odd about all of that. Why wouldn’t the version of JQuery included with WP be working properly?

I would have kept on with my two separate calls for JQuery, but I’ve been having bizarre problems while trying to install several different Nivo Slider plugins. I finally got one to work…but only as long as I left another one active. Troubleshooting led me back to the dual JS issue. Can anybody shed any light?