Since game configuration is handled by a separate application, accessing “Preferences” menu from in-game menu results in switching windows between applications. Unfortunately the game doesn't release mouse control, which means that it is impossible to control the mouse outside the game window. The solution to this problem is accessing the configuration application directly from Windows. To do so, open CONFIG.exe file located in the game directory (“C:Program FilesGOG.comFA-18E Super Hornet” by default) and make all needed changes. Hit “Apply” and “OK”. Launch the game afterwards.