https://gitlab.com/gitlab-com/support-forum/issues/207
https://gitlab.com/gitlab-org/gitlab-ce/issues/26369
https://gitlab.com/gitlab-org/gitlab-ce/issues/21502
Only work around is to create a README on empty repos via the GUI and which then opens up the Protected Branches page. That said the rules around who is able to commit on the repos are broken.
You're right, 3+ weeks is a pretty long time for something like this to be affecting people. Unfortunately I don't have an ETA on when this issue will be resolved, but I'll be keeping tabs on it going forward. Please feel free to add additional comments to the issues if you haven't already, or you can reach out to me directly. Again, I'd like to apologize for any trouble this caused you and others affected by this issue.
Just because Gitlab is not as famous as Github and hackers don't run their botnets on it, it doesn't mean it is safe or stable.