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I am having a very similar problem too! First off I have a 15" Powerbook G4 1.67GHz 1.5GB RAM - I did a format/clean install of Leopard on Saturday and everything on the install went great. I have not noticed any issues with apps working or anything else except... this annoying issue of the wrong window getting the focus. I have also noticed this where I have an Excel sheet open and then open another spreadsheet and instead of the new one I am opening becoming the main focus window it goes back and shows the first open spreadsheet as the focus and the newly opened one immediately behind it! So I constantly having to click to bring focus to the newest window in many apps. Hopefully this will be a simple bug fix for them to cure in the next update.
Besides this annoyance I have not noticed anything simply not working.
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