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I discovered this bug after updating Views recently to 7.x-3.1. Some of my views were not showing all the results that I expected. After looking at the query, I saw that it is because the Views have some joins that are not required (IE: left joins instead of inner joins), but domain_alter_node_query() always does an inner join.
I am using Drupal 7.8 and Domain Access 7.x-2.18.