Just turn off Desktop and Start Menu shortcuts, we know they slow down CCleaner a lot. What is happening is CCleaner has to check to make sure every icon actually goes somewhere which, depending on the number of shortcuts, can take quite awhile. Don't know why this would have manifested only after a Windows Update.
In any case though, the shortcuts don't need to be checked except after you delete files you had links to or uninstalled programs that you some how changed the links for.