@thomasnewyork – If those settings are greyed out as well then something is causing a Fatal PHP error. When that happens nothing that comes after the error continues to process. IE even if our popup were configured correctly, they would never appear because the error is occuring before their supposed to be added to the page.
If that is the case here which it really looks like it is, then your server error logs are likely the only way to know what is happening. WP 4.5 added jQuery 1.12 which could be breaking another plugin causing admin issues as well, but there were a lot of plugins & themes effected by the WP 4.5 changes. Popup Maker was not one of them, except to say that when another plugin or theme causes JS or PHP errors it can / will break our stuff too but that is not something we can control.
Now, to be blunt, from everything you have described, there is a Fatal error occuring and without knowing the error there is really nothing I can do, no way to know where to even start looking.
Hope that helps, but really need to look at the error logs or contact your host and ask them how to view them.