Amer-
That's a very good question. I would have done exactly what you did - watch the aperture setting both with and without the built-in flash on. Did you try it in Av mode? Does it behave differently? In Av the aperture should be entirely your decision. Does the displayed aperture change in different lighting conditions when you're in Tv mode? If it doesn't, it may be that it's showing the maximum aperture and it stops down when you shoot. That would be my guess.