execution plan question

I have a query that accesses a table with a non-clustered index. When I drop the index and run the query, it takes 1.25 minutes to run. With the index, it takes 2 seconds to run. Yet, the execution plan is the same with or without the index. How can that be?
Thank you!

Can you post the query ?

The table that has the added index is called within a function that is being called by the stored procedure. I wonder if this is the problem?
The table has 232,441 rows. It is SQL Server 2005. The number of distinct values for the index is 123,476.
Here is the Stored Procedure:
ALTER PROCEDURE [dbo].[gp_SelectContainerNew]
(
@RequestID int,
@ContainerTypeID int
)
AS
BEGIN
SET NOCOUNT ON

--display Containers
SELECT
C.ContainerBarcode
,PC.PCRCondition
,CONVERT(varchar,C.CreatedDt,101) AS CreatedDt
,SUBSTRING(U1.[User],Charindex('',U1.[User])+1,LEN(U1.[User])) AS CreatedBy
FROM dbo.PCRCondition PC
INNER JOIN dbo.Container C ON C.PCRCondition_id = PC.PCRCondition_id
INNER JOIN View_User U1 ON U1.[User_id] = C.CreatedBy_id
WHERE C.PCRRequest_id = @RequestID AND C.ContainerType_id = @ContainerTypeID AND C.IsActive = 1
ORDER BY C.ContainerBarcode
--display Container SlotsContainerBarcode
SELECT
C.ContainerBarcode
,CSD.Mouse_id
,CSD.TubeBarcode
,CS.Y+CS.X AS Slot
,dbo.GetPrimerPairList(CSD.Container_id, CSD.Slot_id) AS PrimerPairs
,S.Strain
,CS.Y
,CS.X
FROM dbo.Container C
INNER JOIN dbo.XREF_ContainerSlotData CSD ON CSD.Container_id = C.Container_id
INNER JOIN dbo.LOOK_ContainerSlot CS ON CS.Slot_id= CSD.Slot_id
INNER JOIN dbo.XREF_PCRRequestTail T ON T.Mouse_id=CSD.Mouse_id
INNER JOIN Medusa.Medusa.dbo.Geno S ON S.Geno_id = T.Geno_id
WHERE C.PCRRequest_id = @RequestID AND C.ContainerType_id = @ContainerTypeID AND C.IsActive=1
ORDER BY ContainerBarcode,CS.Y,CS.X

END
The table that has the index is in a function that is called within the stored procedure.
Here is the function that contains the table that the index was added to:
ALTER FUNCTION [dbo].[GetPrimerPairList]
(
@Container_id INT
, @Slot_id INT
)
RETURNS VARCHAR(2000)
AS
BEGIN
DECLARE @List VARCHAR(2000)
SET @List = ''
SELECT @List = COALESCE(@List + ', ', '') + P.PrimerPair
FROM dbo.PrimerPair P
INNER JOIN XREF_ContainerSlotDataPrimerPair XP ON XP.PrimerPair_id = P.PrimerPair_id
WHERE XP.Container_id = @Container_id AND XP.Slot_id = @Slot_id AND XP.IsActive=1
RETURN SUBSTRING(@List,3,LEN(@List))
END

Please do not start multiple threads for the same issue.