We did something similar to below example with mongoid 2.0.x and had no problems - with mongoid 2.1.2 (didn't test other 2.1.x releases) relations aren't saved. I can't see anything wrong with my code.

require 'rubygems'
require 'ruby-debug'
gem "mongoid", "= 2.1.2" ## swap for 2.0.2 to make this example work
require 'mongoid'

DB = 'mongoid_failing_example_db'
$conn = Mongo::Connection.new
$conn.drop_database(DB)

Mongoid.configure do |config|
config.master = $conn.db(DB)
end

class Person
include Mongoid::Document
include Mongoid::Timestamps
field :firstname
field :lastname

belongs_to :family

after_create :create_relations

def create_relations
family = Family.first(:conditions => { :name => self.lastname })
if family.nil?
puts "Creating a family"
family = Family.new(name: self.lastname)
family.save
end
self.family = family
save
puts "Saved person instance is now: #

{self.inspect}

"
puts "Finding self is now: #

{Person.find(self.id).inspect}

"
end

end

class Family
include Mongoid::Document
include Mongoid::Timestamps
field :name

has_many :people, dependent: :destroy
end

person = Person.create(firstname: 'John', lastname: 'Smith')
puts ""
puts "after creation Person instance: #

{person.inspect}

"
puts ""
puts "finding that same instance: #

{Person.find(person.id).inspect}

"

1. 1. 1. 1. 1. 1. 1. output using mongoid 2.1.2
                     #Creating a family
                     #Saved person instance is now: #<Person _id: 4e36c7d79eb0710c97000001, _type: nil, created_at: 2011-08-01 15:35:51 UTC, updated_at: 2011-08-01 15:35:51 UTC, firstname: "John", lastname: "Smith", family_id: BSON::ObjectId('4e36c7d79eb0710c97000002')>
                     #Finding self is now: #<Person _id: 4e36c7d79eb0710c97000001, _type: nil, created_at: 2011-08-01 15:35:51 UTC, updated_at: 2011-08-01 15:35:51 UTC, firstname: "John", lastname: "Smith", family_id: nil>
                     #
                     #after creation Person instance: #<Person _id: 4e36c7d79eb0710c97000001, _type: nil, created_at: 2011-08-01 15:35:51 UTC, updated_at: 2011-08-01 15:35:51 UTC, firstname: "John", lastname: "Smith", family_id: BSON::ObjectId('4e36c7d79eb0710c97000002')>
                     #
                     #finding that same instance: #<Person _id: 4e36c7d79eb0710c97000001, _type: nil, created_at: 2011-08-01 15:35:51 UTC, updated_at: 2011-08-01 15:35:51 UTC, firstname: "John", lastname: "Smith", family_id: nil>

1. 1. 1. 1. 1. 1. 1. output using mongoid 2.0.2
                     #Creating a family
                     #Saved person instance is now: #<Person _id: 4e36c8089eb0710f4f000001, _type: nil, created_at: 2011-08-01 15:36:40 UTC, updated_at: 2011-08-01 15:36:41 UTC, firstname: "John", lastname: "Smith", family_id: BSON::ObjectId('4e36c8099eb0710f4f000002')>
                     #Finding self is now: #<Person _id: 4e36c8089eb0710f4f000001, _type: nil, created_at: 2011-08-01 15:36:40 UTC, updated_at: 2011-08-01 15:36:41 UTC, firstname: "John", lastname: "Smith", family_id: BSON::ObjectId('4e36c8099eb0710f4f000002')>
                     #
                     #after creation Person instance: #<Person _id: 4e36c8089eb0710f4f000001, _type: nil, created_at: 2011-08-01 15:36:40 UTC, updated_at: 2011-08-01 15:36:41 UTC, firstname: "John", lastname: "Smith", family_id: BSON::ObjectId('4e36c8099eb0710f4f000002')>
                     #
                     #finding that same instance: #<Person _id: 4e36c8089eb0710f4f000001, _type: nil, created_at: 2011-08-01 15:36:40 UTC, updated_at: 2011-08-01 15:36:41 UTC, firstname: "John", lastname: "Smith", family_id: BSON::ObjectId('4e36c8099eb0710f4f000002')>

As you can see with mongoid 2.1.2 the family_id is nil when finding that person again (and is actually nil in the database). Another thing that is not demonstrated with above code is the fact that we create more complex relations than above and when relating more models AFTER the first one (in this case Family - which fails) the ids get set which is really strange.