I can confirm this is an issue, though I can’t reproduce it with Nicholas’ recipe. Not sure what double-clicking should do, here it works just as single-clicking does (bringing the group of windows to front in the order I left them). Thus I have no recipe to reproduce the issue, here it seems to happen seemingly at random. It is quite frequent though, happens multiple times a day and after it’s triggered nothing short of killall unity-2d-shell fixes it.

I believe this started with the recentmost big Unity updates, 5.4 I think. It wasn’t present in prior versions.