Comment 5 for bug 248769

If it used to work for you in this exact setup, then you were experiencing broken behavior. What you are trying to do is put a 'strut', a window docked on a monitor edge that takes space away from maximized windows, and place it on an 'internal edge', an edge shared by two monitors--in this case, the edge in common between your external monitor and your laptop's screen.

5 years ago when the specification for supporting such struts on multiple monitors was designed, it was unfortunately decided to limit struts to be defined only on the overall virtual screen's dimensions, not relative to any specific monitors in order to keep things a little more backwards compatible. (http://markmail.org/message/ojtfzu6ce5fhr3mp#query:_net_wm_strut_partial%20internal%20edge+page:1+mid:ojtfzu6ce5fhr3mp+state:results)

The last attempt to fix this was in 2004, but died off from lack of interest (http://markmail.org/message/igxshkvtoiftxxaz#query:_net_wm_strut_partial%20internal%20edge+page:1+mid:svlu42opykargpej+state:results).

With the advent of LCD displays with resolutions of 2560x1600, there is a much more significant need for supporting docks on internal edges. With a mjaor distribution like Ubuntu pressing, maybe the specs will be updated to support such a feature.

That said, if the functionality you desire worked before, either you were placing AWN on your bottom monitor or it was a bug with your window manager (Metacity, judging from the screenshots)