After recent upgrade to Jenkns 2.60.3 and GitHub Branch Source Plugin 2.2.3 existing Multibranch Pipeline jobs stopped picking up and creating jobs for PRs. I tried creating a new Multibranch Pipeline job and I see the same behavior there.

The scan repository log lists PRs but it is not displaying the message that indicates a Jenkinsfile was found, as is with a branch. I can also see github hook messages in Jenkns logs.