I have come across something a couple of times that I don't know if its the fault of Atahualpa or a plugin...
Say I have some widgets in the right sidebar... all works fine.. If I activate a plugin that puts another widget area at the top of the widget area list ( like the Overlay plugin by David Hohl) The widgets I had placed in the right sidebar now show up in the widget area labeled "Left Sidebar" ... Functionality has not changed the proper widgets show up in the right sidebar. i.e. The second from the top on the widget page is still the right sidebar, just its label has changed.
The other widget areas are likewise now "mislabeled" and offset by one.