All the calibration kit does is measure the INSTRUMENT error. The GPS method is actually attempting to measure the PRESSURE error, or the POSITION error which is caused by the relative pressure around the pitot and the static ports. I obviously don't know what your plane is, but assuming that it is a fixed wing, then the chances are is that your pitot (or total) pressure error is zero, and that all the pressure error is coming from the static error. It is possible therefore that the pressure error is the same magnitude, but in the opposite sense to your intruemnt error and is thereofre cancelling it out. I suspect the real reason though, is that you cannot really just use one tets point to make a conclusion. The pressure error will probably vary with airspeed, and you really need to cover a wide range of airspeeds to measure the errors properly. In addition, only using one test point, especially with the GPS method, may not be entirely accurate, as it assumes that the weather conditions do not change throughout the runs, and that you have been able to maintain your test airspeed and heading sufficiently correctly throughout.