Did you try to manage your monitors manually in the "Size & Orientation" section, instead of doing that in "Display Configuration"? The first offers in fact some more control. You might try to enable both monitors with their native resolutions, then define the external monitor's position as a "Clone" of the primary one. Check if both are showing your desktop properly. If the external monitor's resolution is smaller than the primary one's (i.e. it doesn't cover the whole desktop), then assign the smaller resolution to both. Finally, try to disable the default monitor in its "Size" field.
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