Comment 2 for bug 642994

I'm not sure this is the same issue but I do often observe new windows not getting focus (not always).
This happens _almost_ systematically with Skype (when you click the tray icon and chose "activate" from the dropdown menu, which opens skype's main window) and occasionally with other programs.
The dock panel shows up with the icon of the new window's application vibrating, but the newly created window doesn't show up (it's somewhere on the background).

By the way, the very same (except there was no dock) used to happen back in 10.10 with gnome, so there's nothing new to me.