Reproduced on Win 7 on 4.0, 4.1, 4.2, 4.3

Initialization errors with prefab instances

To reproduce.
1. Load scene A1. Press Play.
2. Note the console. You should see -
Monkey 1: AWAKE, enabled = False
Monkey 2: AWAKE, enabled = False
Monkey 1: START - WHY AM I BEING CALLED?

In the (really simple) monobehaviours attached to Monkey 1 and Monkey 2, it prints something in awake, and calls enabled = false to disable itself. However, what happens is one of the components somehow magically re-enables itself, and Start gets called on one of them.

This only seems to happen when the topmost object is a prefab, and the objects themselves are prefabs. It doesn't happen at all when you break the prefab connection.

This is broken in Unity 4.1 & 4.2, not tested in other versions.