@toddfadel So you select all layers and record a transparency animation - so all layers fade in and out at the same time. Next step is to change the speed of all layers to maximum - now all fade in and out a little bit faster (1:36).
Now the funny part starts, right? So you have each layer selected and everything is yellow. You start to deselect 1 layer from the group and make the others little bit slower, just briefly and change speed back again to maximum (1:42). This is the moment when the transparency animation starts to offset.
In other words - Imagine 10 people walk with the same speed in a row next to each other. Suddenly 9 people walk a little bit slower and fall back just briefly but start to walk with the same speed again. So 1 guy is in front now and 9 guys a little bit behind. Now 8 walk a bit slower and keep up the speed again etc. etc.
Does this help?