If I remember correctly, they said that something was done to game shape couple seasons ago so, that players with decent stamina would get advantage over guys with low stamina. I may be wrong, though.
Whatever the case, I agree that there's something weird with GPS, particularly in the beginning of the seasons; my starter played 77 minutes and 63 minutes on last two weeks, but his game shape still lags at respectable despite of his respectable stamina.