Sometimes, when we create PR on GitHub - it is ignored by Jenkins. I've tried to re-scan organization - and see in logs:

  Getting remote pull requests...

    Checking pull request #128
      ‘Jenkinsfile’ not found
    Does not meet criteria

But Jenkinsfile is here! I see other bugs in your Jira and here is some additional information:

• Repository is added to Jenkins via GitHub Organization Folder
• We don't use forks
• Commiter is a member of our organization and has full rights on this repository
• Problem PRs are also very simple and doesn't touch Jenkinsfile at all
• Source PR branch has Jenkinsfile
• Branch which we want to merge - was created from source branch and also has Jenkinsfile
• Jenkinsfile was not changed between merge commits
• If I merge branches manually - result has Jenkinsfile
• If we do merge on GitHub UI - result will have Jenkinsfile (and will be built)
• If we recreate same pull request several times - it will be built

And more logs:

Examining our-organization/our-repo:  

Checking branches...  
Getting remote branches...  
  
Checking branch master
      ‘Jenkinsfile’ found
    Met criteria
No changes detected: master (still at 923197f48be5cd8296b8ca95bd72a4a830a474f4)    

Checking branch develop
      ‘Jenkinsfile’ found
    Met criteria
No changes detected: develop (still at 43c2cce36623a4af90b28d886dfb28ea8d813ab8)    

Checking branch feature/198-video-verification
      ‘Jenkinsfile’ found
    Met criteria
No changes detected: feature/198-video-verification (still at 9126f0c6958db3c712078ed0d2587e96004d27c6)  

3 branches were processed  

Checking pull-requests...  
Getting remote pull requests...    

Checking pull request #128
      ‘Jenkinsfile’ not found
    Does not meet criteria

PR #128 - is between develop and feature/198-video-verification - and, as you can see, both have Jenkinsfile and were built successfully.