Okay I have been able to take a look at your site, it seems there were actually two different problems occuring.
1) The “Better WordPress Minify” plugin that is used on your site forces the JS from my plugin to load on all pages, even pages without a comment form. When there is no comment form the JS creates an error. This error is probably what prevented your Piwik tracking snippet from being able to load. (off topic: You should probably load your tracking snippet in the header, not the footer. So long as you use the asynchronous version of the snippet it should not effect your page speed)
2) The way that the “Ajaxed Comments” plugin submitted its comments made it look like all comments were coming from the admin-side, which I was allowing through to fix the bug you reported a few weeks back where you couldn’t reply to comments from the admin area. I have rewrote this part of the logic so that this plugin supports ajax comment submissions properly.
The latest version is now installed on your blog so there shouldn’t be anything that you need to change.
Thanks again for submitting your bugs, and giving me access to your site for testing.