Google Analytics Module not working
I would like to offer an alternative. I  have always had issues with putting my analytics into the analytics module.  I have experienced what you have experienced, plus I question why this code has to go into a module? The fewer modules you have the faster your site performs.

I always get the code from Google and then hard code it into the theme files. In drupal 7, this would go into your html.tpl.php just before the  tag, just as google instructs.  That is called for every single page, so no pages will ever go without it. Plus, it makes your code lighter and one less module to worry about. It has always been the best solution for me.

note: if you are using d6 it would have to go into each page.tpl.php template or its derivative if you have more than that one.  Hope that helps.