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We had to do the following to remove jobs from the queue:
download the jenkins command line interface from your buildserver: http://yourbuildserver/jenkins/cli
java -jar jenkins-cli.jar -s http://yourbuildserver/jenkins/ login --username yourusername --password yourpassword
java -jar jenkins-cli.jar -s http://yourbuildserver/jenkins/ delete-builds Name_Of_Job Build_Number_You_Want_To_Delete