Re-Enable Merged MRs to Close Issues Automatically

How do I re-enable merged MRs to close issues automatically?

Version: GitLab Enterprise Edition 13.1.4-ee

Our MRs used to close the issues that were in the MR description as Closes #12345 for example.

For some reason, now the MRs are merged and the issue is still left open and I need to manually close.

Troubleshooting attempts

I am at a Maintainer level.

I looked at this doc:

But under Settings -> Repository, I already see the box checked for “Auto-close referenced issues on default branch

What other settings should I check or what else should I look at?

Thank you!