Backups are not rotated as defined in settings and takes disk space

Number of backup sets: 3
Clean up differential backups: Checked

However I do see more than 3 full backups and diff backups are not cleaned up.

drwxr-xr-x. 3 jenkins jenkins 4096 2016-08-13 05:03 DIFF-2016-08-13_05-00
drwxr-xr-x. 4 jenkins jenkins 4096 2016-08-13 17:04 DIFF-2016-08-13_17-00
drwxr-xr-x. 4 jenkins jenkins 4096 2016-08-14 05:02 DIFF-2016-08-14_05-00
drwxr-xr-x. 4 jenkins jenkins 4096 2016-08-14 17:04 DIFF-2016-08-14_17-00
drwxr-xr-x. 4 jenkins jenkins 4096 2016-08-15 17:02 DIFF-2016-08-15_17-00
drwxr-xr-x. 4 jenkins jenkins 4096 2016-08-16 18:00 DIFF-2016-08-16_17-54
drwxr-xr-x. 3 jenkins jenkins 4096 2016-08-18 01:34 DIFF-2016-08-18_01-34
drwxr-xr-x. 3 jenkins jenkins 4096 2016-08-13 02:00 FULL-2016-08-13_02-00
drwxr-xr-x. 3 jenkins jenkins 4096 2016-08-14 02:00 FULL-2016-08-14_02-00
drwxr-xr-x. 3 jenkins jenkins 4096 2016-08-16 05:33 FULL-2016-08-16_05-33
drwxr-xr-x. 3 jenkins jenkins 4096 2016-08-18 04:17 FULL-2016-08-18_04-17
drwxr-xr-x. 3 jenkins jenkins 4096 2016-08-18 04:29 FULL-2016-08-18_04-29

In logs I do see multiple:
Aug 18, 2016 4:57:12 AM org.jvnet.hudson.plugins.thinbackup.hudson.model.AsyncPeriodicWork doRun
WARNING: ThinBackup Worker Thread thread is still running. Execution aborted.

Also if I do select "Wait until Jenkins/Hudson is idle to perform a backup" then I am hit with constant "Jenkins is going to shutdown" (ISSUE: https://issues.jenkins-ci.org/browse/JENKINS-33725)
An then see something like:
Aug 18, 2016 4:28:12 AM org.jvnet.hudson.plugins.thinbackup.hudson.model.AsyncPeriodicWork doRun
WARNING: ThinBackup Worker Thread thread is still running. Execution aborted.
Aug 18, 2016 4:28:31 AM org.jvnet.hudson.plugins.thinbackup.utils.Utils waitUntilIdleAndSwitchToQuietMode
Aug 18, 2016 4:28:35 AM org.jvnet.hudson.plugins.thinbackup.utils.Utils waitUntilIdleAndSwitchToQuietMode
Aug 18, 2016 4:28:50 AM org.jvnet.hudson.plugins.thinbackup.utils.Utils waitUntilIdleAndSwitchToQuietMode
Aug 18, 2016 4:29:12 AM org.jvnet.hudson.plugins.thinbackup.hudson.model.AsyncPeriodicWork doRun
WARNING: ThinBackup Worker Thread thread is still running. Execution aborted.
Aug 18, 2016 4:29:47 AM org.jvnet.hudson.plugins.thinbackup.backup.HudsonBackup backupJobsDirectory