Your comments

The non-skippable popup is just awful. Worse, it ALSO blocks any access to the nav menu at the top, you have to refresh and click on something else before the popup comes back.

I don't know what moron thought it was a good idea, but they need fired.

Of course, as soon as your bot-detector is triggered, it stops anything AJAX powered from working, such as the notifications. Frankly this is making your site unusable.