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In addition to the document, are you allowing a reboot after deployment? Do you scan the target machine again before the 2nd deployment attempt?
I don't know what version of Protect you are running, but in Protect 9.2 folders in this location C:\Windows\ProPatches\Staged would indicate a job not starting.
It could be a true scheduler issue, you could take a look at the CL5.log located in the C:\Windows\ProPatches\Logs folder of the target machine and look for the patch file name. If you see it, it attempted to run.
Don't believe any of those apply. A second deployment while changing absolutely nothing is usually successful.
Yes - we always allow for reboots afterwards.
No 2nd scan attempt before the 2nd deployment.
I'll take a look at those logs the next time this happens.
Base on this log, the deployment was scheduled to run at the next boot:
2016-10-27T01:47:01.6113367Z 08c4 I STPackageDeployer.cpp:1287 Scheduling job ('LaunchSTDeployForDeployAfterPreDeployReboot (3cb77b12-b678-4db2-ae1d-50791f2e1c9b)') to launch STDeploy.exe next boot up. . .
2016-10-27T01:47:01.6113367Z 08c4 V SchedClt.cpp:148 CSchedClt(): schedulerType=1, jobCreator=STPackageDeployer, jobName=LaunchSTDeployForDeployAfterPreDeployReboot (3cb77b12-b678-4db2-ae1d-50791f2e1c9b), comment=Pre-deployment reboot - relaunch STDeploy.exe at bootup.
The logs also state Protect successfully initiate the pre-install reboot and the server rebooted.
2016-10-27T01:47:01.6188367Z 08c4 I STPackageDeployer.cpp:1290 Launching SafeReboot. . .
2016-10-27T01:47:01.6188367Z 08c4 I STPackageDeployer.cpp:380 SafeReboot command line: '"C:\Windows\ProPatches\Installation\InstallationSandbox#2016-10-27-T-01-46-20\SafeReboot.exe" -o 3 -requestor 1 -s 2 -i 10 -m 30 -w 10 -n safeReboot.exe -power 4'
2016-10-27T01:47:01.6638367Z 08c4 I STPackageDeployer.cpp:1293 SafeReboot launched; STDeploy.exe will now exit; depending on SafeReboot deployment options, the user may now be interacting with a SafeReboot dialog.
2016-10-27T01:47:01.6838367Z 08c4 S DeployExeStates.cpp:412 Leaving STDeploy::CInitialExecutionPackageDeploy::DoStatefulRemediateActions.
2016-10-27T01:47:01.6838367Z 08c4 I STDeploy.cpp:249 Current remediation phase completed. Process exit code: 0.
2016-10-27T01:47:01.6838367Z 08c4 S STDeploy.cpp:154 Leaving wmain.
Did the system reboot?
When did you collect the logs?
We're going to need a full set of logs here, I think it's time to open a support case. There are too many variable to troubleshoot snippets of specific logs.