I have a job that do PR-builds with ghpr-builder-plugin and there is no any naginator configuration in this job, but it was restarted with "Started by Naginator" reason. I checked plugin code and see no part that can do this.
It really strange, will keep this bug here, maybe somebody else will hit it also. Note: i had this issue twice for old and new jobs.
The only logging that i was able to catch is:

Dec 17, 2014 6:30:48 AM FINE com.chikli.hudson.plugin.naginator.NaginatorListener
about to try to schedule a build in 5 seconds