"When an aircraft is flying at an altitude that is approximately at or below the same distance as the aircraft's wingspan or helicopter's rotor diameter, there is, depending on airfoil and aircraft design, an often noticeable ground effect. This is caused primarily by the ground interrupting the wingtip vortices and downwash behind the wing. When a wing is flown very close to the ground, wingtip vortices are unable to form effectively due to the obstruction of the ground. The result is lower induced drag, which increases the speed and lift of the aircraft.

Low winged aircraft are more affected by ground effect than high wing aircraft. Due to the change in up-wash, down-wash, and wingtip vortices there may be errors in the airspeed system while in ground effect due to changes in the local pressure at the static source."

http://en.wikipedia.org/wiki/Ground_...%28aircraft%29

Flaps increase lift via increasing AOA for the internal section of the wing and, with higher deflection, they increase also drag as braking effect for landing.

I don't think that both ground effect and flaps' effect are much related.