Hi. I have a zero turn mower operating in skid steering mode. I am no expert, but just in observing, I believe that your basic tuning may be off (steering and throttle). I would try to follow the tuning guide here http://ardupilot.org/rover/docs/rover-tuning-steering-rate.html#rover-tuning-steering-rate. The tuning graph is very helpful. I got in a large open field where I had plenty of space. I did my initial tuning of the throttle and then steering in Steering mode. After that, I did most of my tuning in Auto. It would be better if you could have a greater distance between your waypoints when you are trying to tune in Auto. I have 200-300 feet between waypoints in a rectangle as you do.
Mine is not perfect but is working OK for me. It takes a LOT of time.
This thread Skid Steer Mower Overshooting pivot turns is quite long but you may find some useful help down in it.
How are your tuning parameters set? The dataflash log is very helpful to those on here who really know how to look into it also (I am marginal at that).
I am probably not helping you much but I have received a lot of help here and am happy to try!
Also what type of mower do you have?
Good luck!
Kenny