Most likely your situation is this: In changing the rocks, you got rid of most of the natural bacteria in the tank. Now the tank has to cycle again and that cycle causes cloudiness.

Also, I would get that tank away from the window. Natural light is great for tanks, but only when that light is indirect and from across the room and perpendicular. Another cause could, indeed, be excess algae growth in the water from the window.
Knowing how long the tank has been up and what is in it would also help greatly to figure it out.