Suggest going through all options of the Theme Customization to setup (and understand) everything. Check the Menu area to make sure that the theme is selecting the proper menu. Look at the Menus that are defined to ensure you are selecting the correct menu.
Some themes use ‘widget areas’ to allow for different content (including menus) in those areas. Looking at all areas of theme customization is a good place to start.
It may be that plugins are affecting things. Take a look at all plugins to determine their ‘worth’. Update everything to the latest version (WP, themes, plugins). Get rid of old/unused themes/plugins.
If you need information, the googles will usually get you started. But wandering through every option on the WP Admin menu is good for understanding.
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