Maybe you should check the iframe and browser tag in xulrunner. You are probably using iframe tag to start the application, i had the same issue. Just use the browser tag and you will be ok.
EDIT TO EXPLAIN A BIT MORE :
iFrame tag - An inner frame that works much like the HTML iframe element. The src attribute can be used to specify the content of the frame. This content is a separate document.
browser tag - A frame which is expected to contain a view of a Web document. It is similar to an iframe except that it holds a page history and contains additional methods to manipulate the currently displayed page.
When you use iframe tag, google requires you to make additional changes so the tracking works ok. More info : goo.gl/sZz9Mk