I have recently implemented the following Compliance Settings for all my servers: http://gallery.technet.microsoft.com/Reboot-Pending-Check-b943d901#content. This leverages a PowerShell script to check reboot pending status. Of the 250 servers inheriting this, only 1/3 have run the baseline and reported back their status. The other 2/3 have the baseline (seen in the client) but are not running it (see screenshot).
I have confirmed that if I manually run the evaluate task it will execute successfully and report back. All associated Client Settings have Compliance Settings enabled and PowerShell execution policy set to Bypass. The evaluation window on the deployment is set to run on a 4 hour interval. The servers that are not running the check range from Server 2003 - 2012 R2.
Has anyone else seen this before? I have another baseline applied (IPv6 Status Check) that references the registry. It works across all systems.