The Speed up Browsing by Disabling Add-ons popup in IE 11 is really annoying. You can disable the Speed up Browsing by Disabling Add-ons message in IE 11 with this GPO:
Computer Settings -> Policies -> Administrative Templates -> Windows Components -> Internet Explorer -> Disable add-on performance notifications
If the Disable add-on performance notifications GPO isn’t there, then use Turn off add-on performance notifications to disable the Speed up Browsing by Disabling Add-ons message instead. Which version you get will depend on which version of the OS, or more specifically which version of IE you are using on the machine you’re managing the GPO from.