When clicking on Empathy logo with chats open, minimized to tray is undone as well

Binary package hint: gnome-do

This may be broader than just Empathy and not very easy to fix, it's more a usability problem.
When you have chats opened in Empathy, which don't have the focus, and have the userlist minimized to the tray, clicking on the Empathy icon in the GNOME Do Docky bar, all two windows are placed on top of your window stack.

I suggest to only place the window on top that isn't minimized to the tray. Minimizing to the tray is an anologue for putting something away, which means it should stay away unless you explicitly say otherwise.