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The Make Default button in the Customize dialog box is greyed out.
In 3.0 it was possible to set the user Default.apr at both the Extensions Dialog as well as the Customize Dialog boxes. In 3.1 the ability to set the Default.apr is not available from the Customize dialog if any extensions are turned on. After modifying the Arcview GUI with the Customize dialog window choose File/Extensions and unclick all set extensions.
Now the Make Default button at Customize is available. Choose Make Default then go back to File/Extensions and turn back on any needed extensions. Check the Make Default box now and both the extensions as well as all GUI modifications are set in the user Default.apr.