Can't seem to get Mongoid to update references_many associations

mongoid_refmany-issue.rb

class Project
  embeds_many :layers
  embeds_many :maps
end

class Layer
  referenced_in :layer_type, :inverse_of=>:layers
  references_many :maps, :stored_as => :array, :inverse_of=>:layers
  embedded_in :project, :inverse_of=>:layers
end

class Map
  embedded_in :project
  references_many :layers, :stored_as => :array, :inverse_of=>:maps
end

class LayerType
  references_many :layers, :stored_as=>:array, :inverse_of=>:layer_type
end

class LayerController
  def update
    @project=Project.find(params[:project_id])
    @layer = @project.layers.find(params[:id])
    respond_to do |format|
      if @layer.update_attributes(params[:layer])   #Does not fail, but associations not updated
        ...blah...                                  #map_config_ids not set, layer_type_id not set
      else
        ...blah...
      end
    end
  end
end

# Parameters sent to update request

 Processing by LayersController#update as HTML
  Parameters: {"utf8"=>"✓", "authenticity_token"=>"blah=", "layer"=>{"name"=>"Test Layer", "layer_type_id"=>"map-service", "min_zoom_level"=>"0", "max_zoom_level"=>"10", "map_ids"=>["", "test-map"]}, "commit"=>"Update Layer", "project_id"=>"test-project", "id"=>"test-layer"}
editor_development['users'].find({:_id=>BSON::ObjectId('4ce5d8982302c90539000002')}, {}).limit(-1)
editor_development['projects'].find({:_id=>"test-project"}, {}).limit(-1)
Redirected to http://localhost:3000/projects/test-project
Completed 302 Found in 3ms