Farcry 3 randomly enters windowed mode
Solution 1:
If I were to venture a guess, it sounds like your computer is communicating with another program, causing the other program to become the focus, forcing your game into windowed mode. You could try closing other programs, perhaps an overlay program such as Steam or Overwolf could cause this. There are any number of programs that actively listen for hotkeys, such as Skype or Teamspeak.