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Important: Once an entry for a preference setting exists in the user.js file, any change you make to that setting in the options and preference dialogs or via about:config will be lost when you restart your Mozilla application because the user.js entry will override it.

http://kb.mozillazine.org/User.js_file

Он имеет высший приоритет. А точнее:

When you launch your Mozilla application, valid preferences you've added to the user.js file are automatically copied to the prefs.js file (located in the same profile folder) where all user-set preferences are stored. For this reason, you should make a backup copy of the prefs.js file before you create or edit the user.js file.

На старте настройки из него копируются в prefs.js

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Important: Once an entry for a preference setting exists in the user.js file, any change you make to that setting in the options and preference dialogs or via about:config will be lost when you restart your Mozilla application because the user.js entry will override it.

http://kb.mozillazine.org/User.js_file

Он имеет высший приоритет