v11 below.

Select
        ItemCode =S.Code,
        WHCode = W.Code,
        ItemDescription1 =S.Description_1,
        ItemDescription2 =S.Description_2,
        ItemGroupCode =G.StGroup,
        ItemGroupDesc = G.Description,
        ItemWHGroupCode = WS.WHStockGroup,
        --WS.fAverageCost as WHAvgCost,
        --WS.WHQtyOnHand as WHQtyOnHand,
        Qty =
         SUM(CASE WHEN P.Id = 'JCI' THEN -fQuantityInvoiced --JCI invoices directly invoice out, so doesn't affect the available stock qty
                  WHEN P.Id = 'JCS' THEN 0 --JCS is always 0 anyway on the quantity column, so this shouldn't affect anything.
                  /*JCM -> standard rule applies on qty */
                  WHEN P.Id NOT IN ('JCI','JCS') AND Debit > 0 THEN Quantity
                  ELSE -Quantity END)
		,WS.WHQtyOnHand
		,QtyJCWip = SUM(CASE WHEN P.Id = 'JCM' AND Credit > 0 THEN -Quantity ELSE fJCWIPQuantity END)
		,QtyMFWIP = SUM(P.fMFPWIPQuantity)
		,WS.WHJobQty
		,WS.WHMFPQty
		,P.AccountLink
		from PostST P
		LEFT JOIN StkItem S ON P.AccountLink = S.StockLink
		LEFT JOIN GrpTbl G ON S.ItemGroup = G.StGroup
		LEFT JOIN WhseMst W on WhseLink = P.WarehouseID
		LEFT JOIN WhseStk WS ON WS.WHStockLink = P.AccountLink AND WS.WHWhseID = P.WarehouseID
		WHERE /*P.TxDate <='2019/12/31'
			AND */ S.ServiceItem = 0
			--AND P.AccountLink = 164
		GROUP BY
			S.Code,
			W.Code,
			S.Description_1,
			S.Description_2,
			S.ItemGroup,
			G.StGroup,
			G.Description,
			WS.WHStockGroup
			,WS.WHQtyOnHand
			,WS.WHJobQty
		,WS.WHMFPQty
		,P.AccountLink
		HAVING 
			/*Qty diff, QTy on Hand vs Qty in PostST*/
			ABS(SUM(CASE WHEN P.Id = 'JCI' THEN -fQuantityInvoiced --JCI invoices directly invoice out, so doesn't affect the available stock qty
                  WHEN P.Id = 'JCS' THEN 0 --JCS is always 0 anyway on the quantity column, so this shouldn't affect anything.
                  /*JCM -> standard rule applies on qty */
                  WHEN P.Id NOT IN ('JCI','JCS') AND Debit > 0 THEN Quantity
                  ELSE -Quantity END) - WS.WHQtyOnHand) >0.01

;WITH cteStocks as (
SELECT    
    /*Groupings*/
    p.AccountLink as StockID
    ,p.TrCodeID
    ,p.WarehouseID
    ,p.Id as TxId
    ,TxDate
    
    /*Values:*/
    ,QuantityInOut = SUM(CASE 
                    WHEN p.Id = 'JCI' THEN 0
                    WHEN p.Id = 'JCS' THEN 0
                    WHEN p.Id NOT IN ('JCI','JCS') AND Debit > 0 THEN Quantity
                    ELSE -Quantity END)
    ,QtyOut =  SUM(CASE 
                    WHEN p.Id = 'JCI' THEN 0
                    WHEN p.Id = 'JCS' THEN 0
                    WHEN p.Id NOT IN ('JCI','JCS') AND Debit > 0 THEN 0 --Quantity
                    ELSE -Quantity END)
    ,QtyIn =  SUM(CASE 
                    WHEN p.Id = 'JCI' THEN 0
                    WHEN p.Id = 'JCS' THEN 0
                    WHEN p.Id NOT IN ('JCI','JCS') AND Debit > 0 THEN Quantity
                    ELSE -Quantity*0 END)

    --,* 
    from PostST p
	INNER JOIN _as_FM_TrCodes TR ON p.TrCodeID = TR.TrCodeId
    

    WHERE
        1=1
        /*Last 12 months:*/
        AND p.TxDate >= DATEADD(m,-12,(DATEADD(d,1,EOMONTH(GETDATE(),-1))))
    GROUP BY 
        p.AccountLink
        ,p.TrCodeID
        ,p.WarehouseID
        ,p.Id
        ,p.Id
        , TxDate
 --   ORDER BY p.AccountLink, TxDate ASC
)
, cteSummary AS (SELECT StockId, WarehouseId, SUM(QuantityInOut) as SumQty FROM cteStocks GROUP BY StockId, WarehouseId)
, cteStockQty AS (SELECT StockId, WhseId as WarehouseId, SUM(QtyOnHand) as SumQty FROM _etblStockQtys group by StockID, WhseID)
/*Checks with current qty.*/
SELECT * FROM cteSummary s
	FULL OUTER JOIN cteStockQty q ON s.StockID = q.StockID and s.WarehouseID = q.WarehouseId
	WHERE COALESCE(s.SumQty,0) <> COALESCE(q.SumQty,0)
	ORDER BY COALESCE(s.StockID,q.StockId)