do you know how to view your source code from in the browser? Depending on what browser you use... for instance IE you click view -> page source. You can view your page's source output html through each browser
If you view your source code you will see code that looks like this
var _gaq = _gaq || ;
ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
var s = document.getElementsByTagName('script'); s.parentNode.insertBefore(ga, s);
One near the top of your code (that has a comment in it that tells you it's done by Yoast's plugin) and another at the very bottom that doesn't tell you where it's from
Basically, I would kill all plugins and view the source code to make sure they are both gone. Then turn on Yoast's analytics plugin and reload the page and view source to see if only the top analytics code comes back.
Then repeat this process over and over repeating the process to see when that bottom analytics code comes back.
Maybe start off by just deactivating Yoast's plugin, to see if it is accidentally loading the code twice. Basically if you can't tell what is inserting the code, it's all manual testing.