In my experience the holes that get blocked are the ones under the frames that allow the bees into the rhombus, hence the eke under the super being cleared. If you happen to have a frame immediately across the hole it slows the process down. The exit holes are no problem as they only let one bee out at a time and they just filter downwards. Try leaving the eke on for three or four days and see what happens! I speak from experience when I put the eke under the rhombus by mistake this year and then for various reasons didn't remove the board and the eke. I am not saying your way is wrong I am just warning others not to leave it like that for long.