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Sadly not the problem :/
After disabling the original job and re-creating an identical job, I got a failure within 30 mins, exactly the same problem. And this was with a fresh project created under Jenkins 1.606 with no build history.
"jenkins.util.Timer 1" Id=20 Group=main BLOCKED on hudson.diagnosis.OldDataMonitor@27c043dd owned by "Executor #0 for Slave (i-16fd89df) : executing <JOBNAME>l #1" Id=7030
at hudson.diagnosis.OldDataMonitor.remove(OldDataMonitor.java:106)
at hudson.diagnosis.OldDataMonitor.access$000(OldDataMonitor.java:67)
at hudson.diagnosis.OldDataMonitor$1.onChange(OldDataMonitor.java:120)
at hudson.model.listeners.SaveableListener.fireOnChange(SaveableListener.java:80)
at hudson.model.AbstractItem.save(AbstractItem.java:514)
at hudson.model.Job.save(Job.java:177)
at hudson.model.AbstractProject.save(AbstractProject.java:303)
at hudson.model.AbstractProject.setScm(AbstractProject.java:1562)
at com.github.mjdetullio.jenkins.plugins.multibranch.FreeStyleMultiBranchProject._syncBranches(FreeStyleMultiBranchProject.java:1114)
at com.github.mjdetullio.jenkins.plugins.multibranch.FreeStyleMultiBranchProject.syncBranches(FreeStyleMultiBranchProject.java:1018)
at com.github.mjdetullio.jenkins.plugins.multibranch.SyncBranchesTrigger.run(SyncBranchesTrigger.java:98)
at hudson.triggers.Trigger.checkTriggers(Trigger.java:265)
at hudson.triggers.Trigger$Cron.doRun(Trigger.java:214)
at hudson.triggers.SafeTimerTask.run(SafeTimerTask.java:51)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
at java.util.concurrent.FutureTask.runAndReset(FutureTask.java:304)
at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$301(ScheduledThreadPoolExecutor.java:178)
at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:293)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
at java.lang.Thread.run(Thread.java:745)
Number of locked synchronizers = 1