And its usually at the final hour until park closing. THey usually start putting trains away that aren't "supposedly" needed around that time.
As the final hour goes on, the line eventually diminishes to a short wait. On a number of occasions with Indy, when I enter the ride around the last hour, I see the line outside going through the whole outside portion. Then when I come out, the line had amazingly shortened.
I guess once they remove vehciles early, the CM at the loading area has to be quick to make the line faster. From my experience thats been the case.