Ah ha.. I think I missed putting the call to trackTrans() in every footer. I just updated the code on my live site, if it works then I will post the finished contrib (actually I'll just post a patch).

Thanks for the tip

EDIT: Actually it doesn't look like that's the case. One reason I might not be seeing reports yet is because of my subdomain filter. Time to play around some more...

(A side note: it probably doesn't matter that the two scripts are in different <script>tags, does it?)