In my Product.rb

define_index do
    indexes :name, :sortable => true
    indexes brand

    has :id, kosher_id, gluten_free_id, lactose_free_id
    has stores(:id),        :as => 'store_ids'
    has locations(:id),     :as => 'location_ids'
    has categories(:id),    :as => 'category_ids'
    has kosher(:passover),  :as => 'kosher_passover'
  end

In my Searching Class

 def self.for_locations_by_query(query, options = {})
    query, categories = @@coder.decode(query).gsub(/(\b\w+\b)/, "+\
\0"), @@coder.decode(options.delete(:categories))
    origin, page = @@coder.decode(options.delete(:origin)),
@@coder.decode(options.delete(:page))
    per_page, sort_order = @@coder.decode(options.delete(:per_page)),
@@coder.decode(options.delete(:sort_order))
    distance, classifications =
@@coder.decode(options.delete(:distance)),
@@coder.decode(options.delete(:classifications))

    with                        = {}
    with[:store_ids]            = Location.all(:origin =>
origin, :within => distance).collect(&:store_id).uniq unless
origin.blank? or distance.blank?
    with[:category_ids]         = categories.split(',') unless
categories.blank?

    without                     = {}
    without[:kosher_id]         = 0 if
classifications.split(',').include? 'kosher'
    without[:gluten_free_id]    = 0 if
classifications.split(',').include? 'gluten_free'
    without[:lactose_free_id]   = 0 if
classifications.split(',').include? 'lactose_free'
    without[:kosher_passover]   = 0 if
classifications.split(',').include? 'kosher_passover'

    products  = Product.search(query, :with => with, :without =>
without, :per_page => 20, :page => 1)
    stores    = products.collect { |p| p.stores }.flatten.uniq
    locations = stores.collect { |s| s.locations.find(:all, :origin =>
origin, :within => distance) }.flatten.uniq
    locations.sort_by_distance_from(origin)
    locations.each { |l| l.dist = l.distance }

    locations = locations.paginate(:page => page, :per_page =>
per_page)

    return { :total_entries => locations.total_entries, :size =>
locations.size, :locations => locations }
  end

The problematic line is with[:store_ids] = ...
The product can be associated to multiple store ids, however it only
seems to work if the lowest numbered ID is in the array for
with[:store_ids].  For example, the ids associated with product 1000
are [12,15,41], if with[:store_ids] = [15,41] then 0 results are
returned, however if 12 is in the array then it works.

 I have stopped, started, restarted, reindexed, rebuilt, generated a
new conf file for sphinx, and repeated in various orders and I have
had no luck.

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