When you enable default setup, a workflow is triggered with the automatically generated configuration. This run is used to test whether default setup works for all CodeQL-supported languages in the repository.
You can check on the progress of the test run for default setup on the Actions tab. If the run is taking too long, try canceling the workflow run and restarting the configuration process.
To restart your configuration, navigate to the main page of your repository, then click Actions. Click the CodeQL workflow run that's in progress, then click Cancel workflow. Once appears beside the workflow run name, navigate back to the Advanced Security settings and re-enable default setup. If default setup continues to stall, please contact your site administrator or try enabling advanced setup. For more information, see Configuring advanced setup for code scanning.