Thanks for the info! I checked and the issue is the same what I mentioned in above reply. It relates to the multilingual configuration only.
Menus: you set it correctly
Templates: like Menus, you need to have 1 default template style and 1 for EN + 1 for FA - you missed 1 for EN so I created it for you:
The default template style (ja_spa - Default) was assigned to home menu item of FA, this template style loads the main menu for EN so on homepage of FA, nothing showed up.
As I mentioned above, I created a new template for EN and assigned template style of FA to associated menu item of FA. In this new template style (ja_spa - Default fa) >> Navigation >> you need to clone the 'default' navigation to have new ones for each language and assign associated Menu for them respectively:
I did for you and you can apply the same for other languages.