If you're using our special version of the Google Analytics tracking code to enable tracking for cart button clicks, that would replace any other GA tracking code you might use.
We have also seen problems with some WordPress plugins for GA tracking, notably the Ultimate Google Analytics plugin in particular, which rewrites our cart button code after you paste it in a way that breaks the nice overlay-style cart that would appear "inside" your pages.
Speaking of WordPress, you might also be interested in using the WP E-junkie plugin that a fellow client recently developed, which makes adding E-junkie cart buttons to a WordPress site much easier and less potentially problematic:
http://wpejunkie.com/