I had been checking in Keyboard Maestro, BTT, System Settings Keyboard etc, but could not find anything. I just spotted that the “App Shortcuts” section within, Keyboard Shortcuts", within, Keyboard, within System Settings.
That had a shortcut configured for the Hook app for Ctrl-R to execute the Hook menu Rename item. I must have put this in a while ago before you supported a shortcut directly. It seems this seemed to break running your own Ctrl-Shift-R shortcut. Deleting that App Shortcut and your default Ctrl-Shift-R is working.