After some more tests it looks like the problem affects pipeline jobs but 
not freestyle jobs. 
I guess this is a bug so have raised a jira 
https://issues.jenkins-ci.org/browse/JENKINS-41085 

On Wednesday, 11 January 2017 09:59:46 UTC, Joe wrote:
>
>
> Hi all,
>
> I want to run some scripts externally that require that all jobs are 
> stopped.
>
> I expected the following command to stop new jobs being started, and only 
> return once all the jobs in the queue have finished (or reached the end of 
> a stage for pipeline and paused):
> java -jar jenkins-cli.jar -s IP quiet-down -block
> The command does stop new jobs from been started and shows a red banner on 
> the web interface, but the command returns straight away, even when a job 
> is still running. 
> Have I misunderstood the "block" option? 
>
> At the end of the script I was then planning to use: 
> java -jar jenkins-cli.jar -s IP cancel-quiet-down 
> This always removes the red banner from the web UI but sometime the job 
> queue does not restart. 
>
> Using Jenkins version 2.19.4 on Windows 7 running as a service. 
>
> Is there another way to achieve this?
>

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