A simple enough change, but you still need a key row on table1 to know the exact row. See the modified code below as well as my slightly modified table so you can identify the exact culprit rows:

declare @Table1 table

(RowID INT,

id int,

StartDt datetime,

EndDt datetime)

insert into @Table1

select 1, 1,'2009-11-28 00:00:00.000',''

union all

select 2, 1,'2009-11-07 00:00:00.000','2009-11-27 00:00:00.000'

union all

select 3, 1,'2009-07-01 00:00:00.000','2009-11-06 00:00:00.000'

union all

select 4, 1,'2009-06-19 00:00:00.000','2009-06-30 00:00:00.000'

union all

select 5, 2,'2009-11-28 00:00:00.000',''

union all

select 6, 2,'2009-11-07 00:00:00.000','2009-11-27 00:00:00.000'

union all

select 7, 2,'2009-07-01 00:00:00.000','2009-11-06 00:00:00.000'

union all

select 8, 2,'2009-06-19 00:00:00.000','2009-06-30 00:00:00.000'

declare @Table2 table

(id int,

StartDt datetime,

EndDt datetime)

insert into @Table2

select 1,'2008-11-05 00:00:00.000','2009-11-06 00:00:00.000'

union all

select 1,'2007-11-29 00:00:00.000','2008-11-04 00:00:00.000'

union all

select 1,'2007-09-04 00:00:00.000','2007-09-04 00:00:00.000'

union all

select 1,'2007-07-02 00:00:00.000','2007-07-12 00:00:00.000'

union all

select 1,'2006-09-05 00:00:00.000','2007-06-21 00:00:00.000'

union all

select 2,'2008-11-05 00:00:00.000','2009-11-06 00:00:00.000'

union all

select 2,'2007-11-29 00:00:00.000','2008-11-04 00:00:00.000'

union all

select 2,'2007-09-04 00:00:00.000','2007-09-04 00:00:00.000'

union all

select 2,'2007-07-02 00:00:00.000','2007-07-12 00:00:00.000'

union all

select 2,'2006-09-05 00:00:00.000','2007-06-21 00:00:00.000'

;WITH pivotedData AS

(SELECT RowID, id, StartDt as TestDT

FROM@Table1

UNION ALL

SELECT RowID, id, EndDt AS TestDT

FROM@Table1

)

SELECT DISTINCT

pd.RowID

FROM

pivotedData AS pd

LEFT JOIN

@table2 AS t2

ONpd.id = t2.id

AND pd.TestDT >= t2.StartDt

AND pd.TestDt <= t2.EndDt

WHERE

t2.id IS NULL