My configuration settings are

Discover branches -  All Branches

Discover pull requests from origin - Both current and merged with target

Filter by name for master and feature* branches

My pipeline scan log appears to see it

Looking up devts-bb/atlassian-elastic-stack for branches

Checking branch feature/DEVTS-2678-configuration-git-repository from devts-bb/atlassian-elastic-stack
      ‘Jenkinsfile’ found
    Met criteria
No changes detected: feature/DEVTS-2678-configuration-git-repository (still at 4d5d412c8fb56e9446d200287a83007cbc2e03d3)
Checking branch master from devts-bb/atlassian-elastic-stack

      ‘Jenkinsfile’ found
    Met criteria
No changes detected: master (still at 6d0688e7ee81e87b1142183c46e7a8d25fa0c91d)

  2 branches were processed
Looking up devts-bb/atlassian-elastic-stack for pull requests
Checking PR-3 from DEVTS-BB/atlassian-elastic-stack and branch feature/DEVTS-2678-configuration-git-repository

  1 pull requests were processed
[Mon Oct 30 16:47:36 EDT 2017] Finished branch indexing. Indexing took 2.3 sec
Finished: SUCCESS

But the status page of the jobs shows 2 branches and 0 pull requests.

Changing to other combinations of the discover settings does not make a difference.

Let me know what other information would be useful.