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.
what settings are on, usually ARITHABORT
is the culprit, it is ON in SSMS but you might be connecting with it off
Run this in SSMS while you are running your query and see what the first column is for the session that is connected from PHP
select arithabort,* from sys.dm_exec_sessions
where session_id > 50
Run the SQL Profiler, and set up a trace and see if there are any differences between the two runs.