Check to see if the Fooman extension adds a layout file. More than likely, it is adding a second block that is also generating the analytics you reference. Once you find it, you can reconcile the blocks.
Solution 1:
Assuming you are using some kind of custom package, you could copy googleanalytics.xml
from /app/design/frontend/base/default/layout
to your /app/design/frontend/theme/default/layout
folder and simply clear out the references to the googleanalytics/ga
block. The Fooman extension should still output this block and this should take care of your duplication.
<default>
<!-- REMOVE THIS -->
<reference name="footer">
<block type="googleanalytics/ga" name="google_analytics" as="google_analytics" template="googleanalytics/ga.phtml" />
</reference>
<!-- TO HERE -->
...
</default>
Solution 2:
Better, you can copy and modify the fooman layout file to your theme and unset references to the default analytics block by doing something like this:
<default>
<reference name="footer">
<action method="unsetChild"><name>google_analytics</name></action>
</reference>
</default>
I believe both of these methods are kosher; I like the second one better because in the event that you remove the fooman extension, your analytics will automatically be restored without any further effort on your part.