You're still not telling me anything about your setup. Did you download Atmosphere and MissionControl from official sources? What are you doing on the console when the lag sets in etc.Okay, the lag sets in 5 minutes after rebooting the system.
Any other homebrew sysmodules that you might have running in the background. If you're unsure, you could post a screenshot of your atmosphere/contents folder.wdym by what else i am running on my console??
I suggest you delete your atmosphere folder, reinstall atmosphere 0.14.2 and MissionControl from their respective releases on github (don't use any All-In-One packages or anything else from a third party) and see if the problem persists.