There are fewer rows in the table created from a query than expected. More rows are returned when executing the same query on my database.
The ArcObjects components that store the query also take a primary key column name which is used to generate ObjectId's. If this column is not unique, only 1 row is returned per unique value. For example, if a table has 10 rows but only 7 unique values in the unique column, only 7 rows are returned.