We're seeing symptoms that are basically the same as JENKINS-20113 except that we don't have the metadata-plugin installed at all.

Steps to reproduce:
Create a new job
Delete job
(optionally) hit Refresh in the main dashboard
The job still exists

When I watch the file system, I can see the job folder disappearing from the jobs directory, then getting recreated a moment later. This is on Windows, running Jenkins 1.550. We have a second Jenkins server that theoretically has the same configuration and doesn't exhibit this issue, so it "must" be a config problem... but how to diagnose?