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Sometimes when you have many instances of a process, it can get pretty ugly to switch between windows, especially when the windows' names are weird...

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So, is there a setting to sort these pop-up windows alphabetically and not chronologically?

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Not natively.

Two tools come to mind. For multiple console windows, I find using an Expose clone like Switcher for Vista is a far more efficient method.

For the taskbar, try 7 taskbar tweaker which allows you to rearrange toolbars manually. It won't do a alphabetical auto sort however.

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