I was facing a similar problem. This might not fix for your problem, but it could help others that find this topic due to it’s title.
In order to get my prefered lay-out in the WP-admin, I put my fields in a group. I didn’t name the group since I used it entirely for aesthetic purposes. My fields didn’t save either, even though they were all named and labeled. Simply giving the group a name fixed the issue.
ACF Pro version 5.7.2
WP version 4.9.9
