What causes wing vortices? When the wing produces lift, there is higher air pressure underneath it, and lower air pressure on top of it. At the wing tip the high pressure air flips over to the low pressure air, and this creates the rotational element of the vortex, as described in this article. The more lift is generated at the wing tip, the stronger the vortex will be.
Aerodynamic lift is a product of lift coefficient, air density, air speed, and wing area. For subsonic speeds: L = $C_L$ * ½ * ϼ * $V^2$ * A. Only the factor ½ in this equation is a true constant! We have one equation with five variables, so lets have a look at what varies when.
Contrary to our first instinct, wing area is not a constant. Modern aircraft have Fowler flaps at the trailing edge, which are extended outwards and increase the wing area, as well as changing the curve of the wing which increases lift coefficient at a given AoA. So there is the first part of our answer: with deflected flaps we have more wing area to produce a given amount of lift, therefore lower required air pressures, therefore less air flippings at the wing tip :).
The second part of our answer also has to do with flaps. Elliptical lift distribution is only possible when the wing tip has zero AoA, a situation designed to occur in cruise. A clean wing configuration is designed for the cruise condition, where there is lots of airspeed to generate lift and we want to keep induced drag to a minimum. This same clean wing is very ill suited to produce the same amount of lift at the lowest possible landing speed.
CL is a function of angle of attack and of wing shape. The answer with the graph of CL shows CL at constant alpha as a function of flap deflection. A graph of CL at constant flap deflection as a function of alpha would show relatively more lift generated near the wing tip, and that is where the wing vortices are generated. Flaps are located more inboard, meaning that when deflected, a greater portion of the lifting force is generated away from the wing tip.