Mark,
Thanks for letting us know about this. Some plugins may alter the Google Analytics script after our plugin adds it to the page. To avoid this sort of issue, change the Plugin Order so that the Website Optimizer plugin executes AFTER the SEF plugin. The easiest way to do this is to change the ORDER to 9999 in the PLUGIN MANAGER (EXTENSIONS tab in the Administrator), and click the SAVE ORDER icon.
Thanks for pointing this out, we'll update the documentation to include this.