Thanks for your reply.My Logitech GHUB change profile ONLY after at least one ALT+TABing game. Not only in AC but in all games. If u have different settings in AC than in Desktop Default profile it will not load it first. That bug was anoying me recently in COD:MW2, but with mouse buttons that I programmed diferently in Desktop/MW2, but it counts to all Logitech Devices.
If u have second screen its good to have open GHUB to see if it changes profiles when u launch/refocus AC window.