I have a fast running query (sub 1 sec) when I execute the query in SQL Server Mgt Studio, but when I run the exact same query in PHP (on the same db instace) using FreeTDS
Using the LOGIN EVENT (and EXISTING CONNECTION) in SQL Profiler with the Text column will show the connection settings of a lot of important SET commands--Arithabort, Isolation Level, Quoted Identifier, and others. Compare and contrast these between the fast and slow connections to see if anything stands out.