Some people (including me) had noticed that recent Empathy's video calling was breaking with recent GTK+ builds. Some people (not including me) were smart enough to work out the bug was related to client-side-windows.
In CSW-enabled GTK+, calls to GDK_WINDOW_XID() — the function with returns the XID of a GdkWindow — implicitly makes a call to gdk_window_ensure_native() before retrieving the XID. It does this so that there is a window on the X server to return the XID for, and thus ideally no one's application will break under CSW. The problem in Empathy was that the first call to GDK_WINDOW_XID() happened in a thread, which in the olden days would have been harmless, but now it can magically result in your window being allocated server side.
The fix for Empathy (and maybe your program to) is to call gdk_window_ensure_native() as soon as the widget is realized. In Empathy we're calling GDK_WINDOW_XID(), because we don't want to depend on GTK+ 2.18, which looks a lot like this.