The most common mistake done by most of the store owners or even developers that they miss-configure the WooCommerce configuration and in a result the Country field shows as empty.
So first Make sure if you have selected Selling Location as “Sell to Specific Countries Only” from your (WooCommerce -> General) Then you have to select the list of countries in the “Specific Countries” drop down underneath.
WooCommerce over rule the default country fields, this even effect the profile form and the country list will even show’s there as empty.
So you have to either fix this in the function.php file or just list the list of countries the way I have explained above.
hope this may help someone with the latest build of WooCommerce.