They do actually. Red > orange > green > blue. Let it settle.

But there are still bubbles within layers, no?

I'm not sure if the between layers thing might be a similar thing to when bubbles show up on the sides and bottom of a glass of water. Some of the bubbles are also staying because once it's settled down, there isn't enough action to cause them to pop. The constant associated with the surface tension in the sim can also be turned down.