I'm using this setup:
1. primary display on the right (where I can switch between workspaces)
2. secondary display on the left (always with two windows: maximized IRC chat on the top and Empathy roster behind it), only one workspace

When I switch from one workspace to another on the primary display window focus on the second display changes and Empathy roster window pops up above the maximized IRC chat. It's very annoying.

It seems like a feature because it happens only if windows on the secondary screen have different focus on different workspaces. From user's point of view it's really annoying and confusing because you cannot switch between workspaces on the secondary display, windows don't change/disappear either, but focus changes based on switching between workspaces.

Wanted result: Since there is visually only one workspace on the secondary display and all things behave as if there was one workspace, window focus should stay the same no matter what workspace you have on the primary display.

I'm using GNOME 3.2.1, but the same behavior is in GNOME 3.3 as well.