The first thing that comes to mind is the Windows Update service is set to enabled and is running at the time of the deployment. This will cause deployments to take a very long time to process. Our recommendation is to set the Windows Update service to Manual and stop the service to prevent this issue. Verify this first.
Also, are any of these patches .net related?
For the jobs that took a long time there were no .net patches. I did run a job on a server earlier in the day and it only took 15 minutes to install 21 patches (there were .net patches for that job). That server also had the windows update service running.
Unless you ran the exact same patches to the same machine, I don't think that is going to tell us much. I've seen a 1MB patch take an hour to process and 30 patches 30 minutes to process. Some patches just take longer than others, I mentioned .net but there are other patches that can take a long time to process too.
It's going to be very difficult to piece this together like this. I would suggest opening a case with support and provide the entire contents of the C:\Windows\ProPatches folder (minus the patches folder) and we can trace the logs to see how long it took to process the patches.
You should be able to zip and attach the C:\Windows\ProPatches folder (minus the patches folder) to the case.
Please reference this post so I can be assigned the escalation lead on the case.
Let me know if you have any questions.