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Do not change some settings while emulation is running. Many settings won't be changed/saved in that case. When you press F12 emulation is just stopped/paused. Think like on real Amiga that you can't change hardware while Amiga is running.
You need to close and open WinUAE OR press "Restart" button (which appears while running Amiga emulation near "Reset" and "Quit" buttons down left), then you can edit and save configuration for some settings.
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