analytics plugin doesn’t work with certain themes

Has anyone had any issues with the analytics plugin specific to a template. I modified a version of cutline pretty heavily. However the modifications were pretty much just to the CSS to change the look. I did modify the header so it displayed random images.

My issue is that my analytics plugin doesn’t seem to work any longer. In wordpress, it’s active and if I go to my analytics dashboard, it confirms in the setup that it is receiving data. If I view the source, I see the javascript it adds to outgoing links but I don’t see the usual header analytics urchin code. If I switch to my old theme, I then get the header urchin code. I had downloaded a bunch of different themes over time and starting trying them to see if I could replicate the issue. there were a couple where I didn’t get the analytics header code when I did a view source.

Has anyone else experienced this and were you able to resolve it. I can probably just end up redoing the theme but I liked where I had it and it still is weird.

Thanks.