With a fresh table, user.id is starting with value 0. I ran into this issue with MySQL 5 when using the statement:

user.$relatedQuery('locations').then( ... )

knex debugging yields:
...sql: 'select * from GPSLocation where 1 = ?'

Here is my relationshipMappings:

User.relationMappings = {
  locations: {
    relation: Model.HasManyRelation,
    modelClass: GPSLocation,
    join: {
      from: 'User.id',
      to: 'GPSLocation.user_id'
    }
  }
};