Every Joomla template is different. In some cases the template developer has used overrides to change the look/function of a bootstrap menu. When this happens the FontAwesome plugin will cause your menu to break because the plugin uses standard bootstrap classes and overrides the template overrides.
If this is the case, you won't be able to use the function to insert FA icons in menus. We've added a function to easily disable the icon menu function.
Navigate to the Plugin Manager and open the NS FontAwesome Pro plugin. In the Advanced tab you can find a setting to disable the menu icon function.
Currently, the menu/icon function will NOT work with YooTheme templates. It may be added in the future but we do not have an projected completion date at this time.