Sum is an aggregated column, invalid for use in your selection (WHERE clause). One solution is to wrap this on another SELECT. OR:
SELECT
A.JOBNUMBR as [Service Call],
A.PONUMBER as [PO Number],
SUM(A.QTYUNCMTBASE*A.UNITCOST) as [Committed Cost PO],
SUM(B.WS_Committed_Cost) as [Committed Cost WS],
SUM(A.QTYUNCMTBASE*A.UNITCOST) - SUM(B.WS_Committed_Cost) as [Variance]
FROM POP10110 A
LEFT JOIN SV_Costs B
ON A.JOBNUMBR = B.Service_Call_ID
AND A.PONUMBER = B.Reference_TRX_Number
AND B.WS_Committed_Cost <> 0
WHERE A.Product_Indicator = 3
AND A.QTYUNCMTBASE <> 0
GROUP BY A.JOBNUMBR, A.PONUMBER
HAVING (SUM(A.QTYUNCMTBASE * A.UNITCOST) - SUM(B.WS_Committed_Cost)) <> 0
ORDER BY A.JOBNUMBR, A.PONUMBER