@laura. Thanks for posting. My plugin runs on every page. So, if the pop ups work on all the other pages and not on the home page, most likely, something is going on on the home page. Also, when i have visual problems like this, i usually check the browser’s console for error messages. You should practice that too. When i did so of your site, I see that following screen. I think that the problem you are having has to do with this error:
Blocked a frame with origin “https://clickberry.tv” from accessing a frame with origin “http://www.youtube.com”. The frame requesting access has a protocol of “https”, the frame being accessed has a protocol of “http”. Protocols must match.
Also there is nothing in the Google Analytics javascript code that should interact with the JCE Mediabox code. Also, I didn’t write the Google Analytics javascript code. It is code that Google provides.
The only other thing I can think of is for you to turn off the Outbound Links feature. You can do this by setting “Enable Event Tracking” to No. Maybe when Google tries to track outbound links, it causes a conflict with the external videos and the different protocols, as specified in the error above. Try it and let me know what happens.