If you have an upgraded database and utilize the built-in Query Editor, you may want to enable the 'QUERY BY FORMULA uses SQL Joins' compatibility option.

When this feature is turned off, a related query performed from the Query Editor can become a Sequential Search. Enabling this feature allows the Query Editor to perform SQL Joins for relational queries. The SQL Join can drastically speed up the relational query.

To enable this setting:
Go into the Database Settings, Compatibility tab, and check the box for 'QUERY BY FORMULA uses SQL Joins'