In ConfigMgr world, one must learn patience – in particular when installing hotfixes, service packs and cumulative updates. It is quite common for the installer GUI to complete and leave you under the false pretense that your environment is ready to go again, but what you will find is that the installer has triggered additional tasks which the SMS/ConfigMgr component manager needs to handle.
I would certainly recommend using trace32/cmtrace to watch the sitecomp.log when you are performing updates to your environment as this will give you an idea as to whether the component manager is initiating a re-installation of certain site components following an update. You may see a flurry of activity which mentions the re-installation of components and the SMS_SERVER_BOOTSTRAP service. When this log has settled back down to normal then you can think about returning your environment to normal usage.