Double-check that Bootcamp.exe is running by looking in the System Tray for the black diamond icon. If it's not running, start Boot Camp in Windows by running
C:\Program Files\Boot Camp\Bootcamp.exe.
Once Boot Camp is running, you can right-click the System Tray icon and open the Boot Camp Control Panel, then use the options in the Keyboard tab to configure your computer.
If the Fn keys stop working when you reboot, you need to add Boot Camp to Startup Items by opening
%USEPROFILE%\AppData\Roaming\Microsoft\Windows\Start Menu\Programs\Startup, and dragging & dropping a shortcut to Bootcamp.exe in there. You can create a shortcut by locating the actual Bootcamp.exe file, right-clicking, and selecting Send to Desktop (Create Shortcut).