I am having a similar issue. I'm using the WooCommerce plugin with a custom designed theme. I can see in the view source of the confirmation page that the Google Analytics code is firing and all of the order data is being captured, however, nothing is getting reported to Google. All of my other (non-transactional) analytics are working fine.
Like some of the earlier posters, I see the <p> tags surrounding the analytics code. I don't know if that is having an effect or not.
I am running the latest version of the plugin.
Any help is appreciated.