Problem description: 
The Keyboard tab of the Customize dialog has no optimal usability. It is not obvious what to do, it is not obvious what selection will make a change.

Assuming an action has already a shortcut (subscript, Ctrl+Shift+B), and the user wants to change it to Ctrl+Shift+H:

Steps to reproduce:
1. Open the Keyboard tab in the Customize dialog.
   From top to bottom:
2. In Shortcut keys, select the new keyboard shortcut Ctrl+Shift+H
3. In Functions, select the category "Format" and the function "Subscript"
(4. Then you would want to click "Modify")

Current behavior:
Once you click something in "Functions", the selected shortcut key gets unselected.

Expected behavior:
It should not change your selection as long as you are in the process of selecting a shortcut & function and click the button.

This workflow is inverted. As a minimum, the "Functions" section should be above "Keyboard shortcuts" so that the user selects them in the correct order.
The whole dialog would better be redesigned. A list of all combinatorial combinations of A-Z, Shift, Ctrl, Alt etc. is too long. It would be better oriented on how other (more modern) applications are nowadays implementing such a feature.
Operating System: Ubuntu
Version: 4.0.1.2 release