First there are some problems with your frame you need to look into.
The output of motors motors 1,3,6 (Clockwise rotation) are constantly MUCH higher than motors 2,4,5 (Counter-clockwise rotation).
Most of the time, half of your motors are running at minimum power and all the lift is coming from the other three motors.
This means the hex is constantly trying to yaw and the flight controller is compensating heavily.
You can see this if you plot RCOU.C1 through RCOU.C6
Check for twist in the arms and that you are using matching propeller sizes / makes and motors.
Once this is corrected, if you still have problems landing you could also look at http://ardupilot.org/copter/docs/ground-effect-compensation.html , although this should probably be the last step.