Cakes cooked in same tin but come out different sizes
There are a few things that can affect the rise of the layers.


If you're baking multiple layers at once, even if your oven heats evenly, the cake on top will rise less than the one of the bottom.  The problem is that the top will crust, preventing the top layer from rising as high as the one underneath which is shielded from the radiant heat.
If you're mixing a large batch of batter, then dividing it between pans, the amount of batter in each pan might be slightly different from each other.  If you're beating it individually, the amount of time that you mix it can affect the rise -- too much mixing will develop gluten which can impede the rise. 
If you're baking the layers individually, you run into the problem that the oven might have been different temperatures, or at least have absorbed a different amount of heat if the oven wasn't preheated for a sufficiently long time. The result is that the later layers tend to rise a little bit less, as the top sets a little bit earlier.
If you're baking the layers individually, but mixed the batter in one batch, then the leavening might not have quite the same strength as in the first batch, and reduce how well it rises ... which has the top set even faster, further reducing the rise.


One other possibility that I haven't tested is if you take things out of the fridge and leave them out while you're baking the other layers.  As the eggs and milk might now be between fridge temp and room temp, that slight change might affect the rise as well.