Ftyjtk

I have two simple queries that execute within expected time when they run alone.
The first query:

SELECT OBJECTID AS OID FROM PST_35053_SNAPPED;

Takes less than a second and returns about 3000 rows.
The second query:

SELECT DISTINCT PST.OBJECTID as OID FROM PST_35053_SNAPPED 

PST INNER JOIN  POWNERS_35053 POW

ON geometry::STGeomFromText('POINT(' + convert(varchar(16),POW.x) + ' ' +

convert(varchar(17),POW.y) + ')', 2100).STWithin(PST.Shape)=1;

Takes a second returning about 2500 rows.

When combining them with EXCEPT to retrieve polygon IDs without points falling in them (about 500 rows), the resulting query takes more than two minutes to execute (about 122 seconds):

SELECT OBJECTID AS OID FROM PST_35053_SNAPPED

EXCEPT

SELECT DISTINCT PST.OBJECTID as OID FROM PST_35053_SNAPPED 

PST INNER JOIN  POWNERS_35053 POW

ON geometry::STGeomFromText('POINT(' + convert(varchar(16),POW.x) + ' ' +

convert(varchar(17),POW.y) + ')', 2100).STWithin(PST.Shape)=1

Is there something I am missing or doing wrong?
I am using SQL Server 2012 SP3

Try to insert your script to temp table than combine it. We don't have execution plan we can only show you to execute your query with different angles. :

SELECT DISTINCT PST.OBJECTID as OID INTO #Temp FROM PST_35053_SNAPPED 

PST INNER JOIN  POWNERS_35053 POW

ON geometry::STGeomFromText('POINT(' + convert(varchar(16),POW.x) + ' ' +

convert(varchar(17),POW.y) + ')', 2100).STWithin(PST.Shape)=1;



SELECT OBJECTID AS OID FROM PST_35053_SNAPPED

EXCEPT

SELECT OID FROM #Temp;

or try not exists :

SELECT OBJECTID AS OID 

FROM PST_35053_SNAPPED PST1

WHERE NOT EXISTS 

    (SELECT 1 FROM 

        (

            SELECT DISTINCT PST.OBJECTID as OID FROM PST_35053_SNAPPED 

            PST INNER JOIN  POWNERS_35053 POW

            ON geometry::STGeomFromText('POINT(' + convert(varchar(16),POW.x) + ' ' +

            convert(varchar(17),POW.y) + ')', 2100).STWithin(PST.Shape)=1

        ) PST2

        WHERE PST1.OBJECTID=PST2.OBJECTID

    )

or try WITH :

WITH Cte AS 

(

    SELECT DISTINCT PST.OBJECTID as OID FROM PST_35053_SNAPPED 

    PST INNER JOIN  POWNERS_35053 POW

    ON geometry::STGeomFromText('POINT(' + convert(varchar(16),POW.x) + ' ' +

    convert(varchar(17),POW.y) + ')', 2100).STWithin(PST.Shape)=1

)

SELECT OBJECTID AS OID FROM PST_35053_SNAPPED

EXCEPT

SELECT OID FROM Cte;

It's hard to say without query execution plan.
However, if I understand correctly, the following query should get the same result, and would be faster.

SELECT PST.OBJECTID as OID 

FROM PST_35053_SNAPPED PST 

LEFT JOIN  POWNERS_35053 POW

ON geometry::STGeomFromText('POINT(' + convert(varchar(16),POW.x) + ' ' +

convert(varchar(17),POW.y) + ')', 2100).STWithin(PST.Shape)=1

WHERE POW.OBJECTID IS NULL