Steps to Reproduce:

• Setup a JIRA instance and connect it to a database (tested it with PostgreSQL)
• Update the sequence_value_item table:

  UPDATE sequence_value_item
     SET seq_id=10400 WHERE seq_name='FieldConfiguration';
  

  The purpose of this is to make FieldConfiguration and FieldConfigScheme of different value. By default, they are the same.
  

• Restart JIRA to pickup the new values set from the database
• Create a project and select list custom field.
  *Create issues and specify values for the select list custom field
• Backup the instance
• Delete all issues from the project
• Perform project import

If you look into the issues that were created with the select list custom field value, you would notice that the value has not been restored.