Hi!
Thank you very much for the details, it helps me a lot!
It is very likely due to the fact that those custom fields are not yet used anywhere, only registered with ACF. The search plugin uses the post meta database to look for the custom field names, however if the custom field is never used, it won’t be able to find it. Once you add the field with a value to a post, it will be visible.
You can still type it in and use it though: http://i.imgur.com/IDuHzEY.png
I hope this helps 🙂