Rest API v2 has to be set after each start of SCM-Manager as it is not stored in the JIRA configuration file (/var/lib/scm/config/jira.xml on my Debian system)
I can't reproduce the issue, after changing the checkbox the value of the jira configuration changes:
Do you change the global configuration or a repository configuration?
I just figured out what went wrong.
The scm-manager did not have write permissions on the configuration file. This was also logged to scm-server.err
java.io.FileNotFoundException: /var/lib/scm/config/jira.xml (Permission denied)
but not shown in the UI after clicking on "Save".
After correcting the permissions the configuration file was updated with the <rest-api-enabled> line.
This was an administrative error.