Avoid SQL Pivot returning duplicate rows

EDIT: I missed the root-cause of your issue being the inclusion of the periodname column causing the percieved duplication. I am leaving this in place as general solution showing CTE usage, because it could still be useful if you then want to do extra filtering/transformation of your pivot results

One way is to take the results of the pivot query and run it through a SELECT DISTINCT query.

An example of wrapping your pivot query as a CTE and using it to feed a SELECT DISTINCT below (please note: untested, but parses as valid in my SSMS)

WITH PivotResults_CTE (
    stockcode,
    description,
    pack,
    location,
    lname,
    qty,
    StockCode2,
    periodname,
    months,
    saleqty
)
AS (
    SELECT *
    FROM (
        SELECT X.stockcode
            ,X.description
            ,X.pack
            ,X.location
            ,X.lname
            ,X.qty
            ,Y.stockcode AS StockCode2
            ,y.periodname
            ,Y.months
            ,Y.saleqty
        FROM (
            SELECT dbo.stock_items.stockcode
                ,dbo.stock_items.description
                ,dbo.stock_items.pack
                ,dbo.stock_loc_info.location
                ,dbo.stock_locations.lname
                ,dbo.stock_loc_info.qty
            FROM dbo.stock_locations
            INNER JOIN dbo.stock_loc_info ON dbo.stock_locations.locno = dbo.stock_loc_info.location
            LEFT OUTER JOIN dbo.stock_items ON dbo.stock_loc_info.stockcode = dbo.stock_items.stockcode
            WHERE (dbo.stock_items.STATUS = 's')
            ) AS X
        LEFT OUTER JOIN (
            SELECT dbo.dr_invlines.stockcode
                ,(12 + Datepart(month, Getdate()) - Datepart(month, dbo.dr_trans.transdate)) % 12 + 1 AS Months
                ,Sum(dbo.dr_invlines.quantity) AS SaleQty
                ,dbo.period_status.periodname
            FROM dbo.dr_trans
            INNER JOIN dbo.period_status ON dbo.dr_trans.period_seqno = dbo.period_status.seqno
            LEFT OUTER JOIN dbo.stock_items AS STOCK_ITEMS_1
            RIGHT OUTER JOIN dbo.dr_invlines ON STOCK_ITEMS_1.stockcode = dbo.dr_invlines.stockcode ON dbo.dr_trans.seqno = dbo.dr_invlines.hdr_seqno WHERE (STOCK_ITEMS_1.STATUS = 'S')
                AND (
                    dbo.dr_trans.transtype IN (
                        1
                        ,2
                        )
                    )
                AND (dbo.dr_trans.transdate >= Dateadd(m, - 6, Getdate()))
            GROUP BY dbo.dr_invlines.stockcode
                ,Datepart(month, dbo.dr_trans.transdate)
                ,dbo.period_status.periodname
            ) AS Y ON X.stockcode = Y.stockcode
        ) z
    PIVOT(Sum(saleqty) FOR [months] IN (
                [1]
                ,[2]
                ,[3]
                ,[4]
                ,[5]
                ,[6]
                )) AS pivoted
)
SELECT DISTINCT *
FROM
    PivotResults_CTE
; 

Also note, your sql included in the above may look slightly different to your original but that is only because i ran it through a reformatter to ensure i understood the structure of it.

In other words, the basic CTE wrapper for your pivot query is:

WITH PivotResults_CTE (
    Field1,
    Field2,
    ...
)
AS (
    YOUR_PIVOT_QUERY_HERE
)
SELECT DISTINCT *
FROM
    PivotResults_CTE
;