My dad, who is the chair of a polisci department, says that often times these schools that do the waves of rejections are waiting to figure out if they'll be able to fund one or two more. It's also possible that they're figuring out their waitlists. UVa is the classic example: they send out three or four acceptances for the fellowship nominations and once they have the results of that and some responses form the applicants, they return to the pile to see who else they can afford funding for. I still think it's hugely inefficient to do it this way, especially since they all know about grad cafe, buuuut I guess I sorta get it...