Numinex module users:
Make sure your copy of "/admin/configuration.php" includes code calling the defined "use_function" for configuration options. While only a handful of core Zen Cart configuration options define a "use_function", many of the configuration options for Ultimate URLs make use of the "use_function".

The stock Zen Cart code calls the "use_function" (if defined for a configuration option) to determine the correct "value" to display for a configuration option. The stock Zen Cart code calls the "use_function" every time the configuration page is displayed (and leaves room for more creative uses than just display).

Ultimate URLs uses the "use_function" to fire additional "events" (such as checking for valid options / combinations of options). These events in turn "save" the updated / changed configuration options to the database (for Ultimate URLs).

This means if the code in "/admin/configuration.php" does not call the defined "use_function" (at least once), one will not be able to configure Ultimate URLs using the standard Zen Cart "admin"->"configuration"->"Ultimate (SEO) URLs".

Note: A special thank you to DivaVocals for directing me to the exact reason for the compatibility conflict between some of the Numinex modules and Ultimate URLs.