Windows services (windows update and others) leaves the system slow;
Updating cis after version 10 may have something to do with it;
but the cause may be even windows (1809) or incompatibility between the system and the CIS.
Can you please check the regkey again in HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows\CurrentVersion\RunOnce or HKEY_CURRENT_USER\SOFTWARE\Microsoft\Windows\CurrentVersion\RunOnceand see if there is “StopServiceRestart” key?
And while the coputer is slowly booting can you enter Task Manager and see if you have a process called “StopService.exe” running?