I found out that the maintenance window for a device is set by the default agent setting and is not overridden by selecting a different Distribution and Patch setting. To scan and avoid a maintenance window you have to schedule the task from the Patch and Compliance component. Click on the Calendar icon on the toolbar then select "Security Scan". In the window that appears you need to check the box "Ignore maintenance window if specified". Then select the agent settings you want to use if needed. You will then have a scheduled task you can run for any of the machines that you need to run a security scan on. If you look under the "Message" column after starting the task you will see where it is at in the scan process and it will show how many patches it has installed and how many total are needed.
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