File query alteration conflicts with OG

When used with Organic Groups, file_entity_query_entity_field_access_alter() causes a fatal "column not found" error on certain entity field queries. In particular, this causes major problems with Open Atrium. As best I can tell, this is what's happening:

The query that causes the error starts off as something like:

SELECT field_data_og_group_ref0.entity_type AS entity_type, field_data_og_group_ref0.entity_id AS entity_id ...
FROM  {field_data_og_group_ref} field_data_og_group_ref0 ...

_file_entity_query_file_entity_access_alter() does a bunch of stuff, and ultimately adds a field_data_og_group_ref0.entity_id = fm_access.fid into the WHERE clause of a subquery.

Later, og_query_og_membership_alter() seems to be changing the table name/alias in the outer query to {og_membership} ogm, but the subquery condition stays the same, causing the Column Not Found error.