Reproduced Scenario:

• Environment: Jenkins 1.642.4.2, GitHub Organization Folder Plugin 1.2, Pipeline (aggregator) 2.0

• A webhook is properly created between a Github Organization and the described Jenkins environment.

• After Re-scan Organization > Run Now all the repositories and associated branches containing Jenkinsfile are properly discovered.

• If a repository has previously been discovered: (It had a Jenkinsfile in one of its branches when the folder computation was last run) Everything works fine, if push to new branches with a Jenkinsfile are applied, new jobs are created in Jenkins for that repository.

• If a repository has NOT been previously discovered (the repo didn't exist or didn't have a Jenkinsfile). In that case, even if you push a Jenkinsfile to the repo, it doesn't get discovered automatically. In case you proceed manually to Re-scan Organization > Run Now yes they are discovered.

Notes:
(1) The webhook seems to work fine. So it is not related to the communication between the Github Organization and the Jenkins instance.