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It must be for specific few systems first you need to check the services in those systems .
What services should I check?
When the deployment is run on this system can you remote into it and check to see if Windows installer process is running or if you see the image name listed in task manager/processes for any of the patches that were deployed?
If you do see these processes running then it means the installation is in progress.
Also, on the target system check in C:WindowsPropatchesInstall - sort so you have newest files first, and then of the newest files do you see a .bat or .HIS file?
.bat will indicate that the installation has not been kicked off by the scheduler service.
.HIS will indicate that the installation process has been started/has run.
I think I may have found the issue. I know in the latest XML, Vmware disabled this patch, MS13-036. The patch still shows up in the scan, but does not deploy. This is expected behavior. However, on some machines, when this patch is selected, deployment of all the other patches fails as indicated in the screenshot I originally posted. That is, deployment is complete while some machines still show "in progress." If I deleselect this patch, and deploy the other patches that never were pushed out, deployment is successful, patches are copied to target machine and installed without incident. Not sure why this deployment oddity only occurs with some machines, but the workaround I have outlined should help.