After upgrade to SP3, I have many duplicate queries in the Public queries section. All of them start with CI, example: CI Blade Server Query, CI Device query, etc. The show up under every folder that is created in the Public queries section. If they are deleted and the console refreshed they come right back. If I try to delete them from the web console, I get an access denied.
Create a folder within "Public queries" called '!queries (cannot delete)". Move the ghost queries to this folder and then delete the folder. This worked for me and they have not shown up.