There’s a focus bug in the latest Ubuntu (basically, in the Compiz package, but who cares about specifics ;-). Basically, if you select “focus follows mouse”, your mouse will uniquely determine the focus. Always. Previously, the mouse would only change focus on window entry.
In other words: Alt+Tab only works in the new Ubuntu if the mouse isn’t over any window. Which is usually not the case.
Bug report here. I hope it gets fixed soon, it annoys me daily – I use Alt+Tab. Often. :s