Warning: The changes made to your preferences will not be retained next time you save because the top-level module is a linked module or linked library. Preferences are saved with Models, not with linked models.
You have a Module or Library loaded, rather than a Model. Since preference settings are stored in Model files, and not in Module or Library files, the changes you just made from the Preferences dialog will not be retained after you have saved and reloaded your work.
This does not apply to the settings in the Personal Preferences section of the Preferences dialog, since these are never stored with the model file. Changes to Personal Preference are retained.
The changes you have made will take effect while you have you have the Module loaded.
If your module or library is used by another model, then load that model instead and change the preferences. The new settings will then apply to that model.
If you want the module that you have loaded to be used alone, and hence, to retain its own preferences, then you should change it to be a Model instead. To do this, bring your top-level diagram to the front, and open its Object Window. Make sure you are in edit mode, and change the object class to Model using the pull-down in the top-left corner.