When you land a vessel, it remains "in-flight state" unless it is perfectly stationary with no thrusters firing for 5 seconds, and then it goes into "landed state". When landed, the vessel will remain fixed on the surface, but if it is still "in-flight", time acceleration will make it jump and sayonara (the aero, gear mechanics and orbital mechanics simply aren't stable with a very low sampling).
The (best) way you can change the vessel state to "landed" is by putting the brakes on for 5 seconds, and you should see the AOA meter in Surface MFD the stop moving = you are now in "landed state".