Hierarchy rearranges itself

In Unity 5, I started noticing that when I open a project, it's hierarchy has been almost completely jumbled, the only thing I can rely on is parent/child relationships. This hasn't been a problem for a while, as order in the hierarchy doesn't matter unless you look for children by index.

Unity UI layers it's elements based on it's order in the hierarchy. Every time I open my project, my UI layering is completely ruined by the randomly jumbled hierarchy! Words cannot describe how...

Hierarchy rearranges itself