Love your work.
Spoke with Adam Czajczyk yesterday via chat and he gave me some tests to validate why the PopUp was loading the page it appear on into the PopUp. I created a test page and REMOVED the SiteOrigin plugin and the WPMU pop is working correctly. When SiteOrigin is installed on the page, PopUp fails.
Here is the page without SiteOrigin. Success!
Here is the same page with SiteOrigin installed. Fail!
Adam asked me to send the result in case it's something you can fix on your end. If not, let me know and I will contact SiteOrigin to diagnose the issue.