I just did a test with your field groups. I imported the groups into a site with only ACF installed and using and unmodified version of Twenty Fifteen. Everything seems to be working.
You say that the defaults are not selected when you add an new layout. The layout is added using JavaScript, so there may be an error happening in JS that’s causing the issue. Check to see if you see any JS errors.
There have been some reports of JS issues that started in WP 4.6. This has been reported to the developer and should be fixed in the next update. What version of WP are you using? What version of ACF do you have installed?
Try deactivating other plugins or switch to one of the default WP themes. Let me know if any of this corrects the problem.
