I am experiencing the exact same issue and it’s very frustrating. I will create an event in Events Calendar and register it with Eventbrite. It works and the Eventbrite reg shows in the iFrame on the page. But when I go back to the event in WP to make an update the “Register this event with eventbrite.com” radio buttons are both unchecked.
WP 4.7.3
Events Cal Pro 4.4.4
Events Cal Eventbrite 4.4