Here's the full code. I don't think the rest of it would affect the results, but you tell me?
Select S1.*, S2.Cnt, Cast(Null as Integer) as rn
Into AS_Workspace.dbo.StdPmt_InvAmt_SUM7
From FSW_NZ_JDE_Apr05_Sep12_C.dbo.StdPmt as S1
Inner join ( Select VndNbr, InvNbr, Sum(InvAmt) as InvAmt_Sum, Count(*) as Cnt
From FSW_NZ_JDE_Apr05_Sep12_C.dbo.StdPmt
Group By VndNbr, InvNbr) as S2
ON S1.InvNbr = S2.InvNbr
AND S1.VndNbr = S2.VndNbr
AND S1.InvAmt <> S2.InvAmt_Sum
AND S2.InvAmt_Sum > 0
Where S2.Cnt = 2
UNION
Select S1.*, S2.Cnt, Cast(Null as Integer) as rn
From FSW_NZ_JDE_Apr05_Sep12_C.dbo.StdPmt as S1
Inner join ( Select VndNbr, InvNbr, Sum(InvAmt) as InvAmt_Sum, Count(*) as Cnt
From FSW_NZ_JDE_Apr05_Sep12_C.dbo.StdPmt
Group By VndNbr, InvNbr) as S2
ON S1.InvNbr = S2.InvNbr
AND S1.VndNbr = S2.VndNbr
AND S1.InvAmt <> S2.InvAmt_Sum
AND S2.InvAmt_Sum > 0
Where S2.Cnt > 2
AND NOT EXISTS(Select InvAmt
From FSW_NZ_JDE_Apr05_Sep12_C.dbo.StdPmt as S3
WhereS2.InvNbr = S3.InvNbr
AND S2.VndNbr = S3.VndNbr
AND S2.InvAmt_Sum = S3.InvAmt )
UNION
Select S1.*, S2.Cnt, Cast(Null as Integer) as rn
From FSW_NZ_JDE_Apr05_Sep12_C.dbo.StdPmt as S1
Inner join ( Select VndNbr, InvNbr, Sum(InvAmt) as InvAmt_Sum, Count(*) as Cnt
From FSW_NZ_JDE_Apr05_Sep12_C.dbo.StdPmt
Group By VndNbr, InvNbr) as S2
ON S1.InvNbr = S2.InvNbr
AND S1.VndNbr = S2.VndNbr
AND S1.InvAmt = S2.InvAmt_Sum
AND S2.InvAmt_Sum > 0
Where S2.Cnt > 0
UNION
-- Insert records to get Invoices with more than 2 records that don't equal 0 and have a negative amount of the sum of invamt.
--Pull in 1 of the 2 Negative records.
--Insert Into AS_Workspace.dbo.StdPmt_InvAmt_SUM2(VndNbr, VndName, InvNbr, InvDt, InvAmt, NetAmt, FInvAmt, DiscAmt, FDiscAmt, TaxBaseAmt, GSTAmt, FGstAmt, InvCurCd, InvStat, PmtTrms, BatNbr, PONbr, CstCntr, Cmpy, VchNbr, TrTyp, Descr, TaxCd, AdjDoc, Void, chknbr, ChkAmt, ChkCurr, ChkDt, ChkClearDt, ChkTyp, VndBnkAcct, AmtPaid, Chk_payId, ChkBatNbr, void_gl_date, VatPct, DiscPct, Cnt, rn)
Select *
FROM (
Select S1.*, S2.Cnt , rn = ROW_NUMBER() OVER (PARTITION BY InvAmt_Sum ORDER BY ChkNbr DESC)
From FSW_NZ_JDE_Apr05_Sep12_C.dbo.StdPmt as S1
Inner join ( Select VndNbr, InvNbr, Sum(InvAmt) as InvAmt_Sum, Count(*) as Cnt
From FSW_NZ_JDE_Apr05_Sep12_C.dbo.StdPmt
Group By VndNbr, InvNbr) as S2
ON S1.InvNbr = S2.InvNbr
AND S1.VndNbr = S2.VndNbr
AND S1.InvAmt = S2.InvAmt_Sum
Where S2.Cnt > 2
AND InvAmt_Sum < 0
) NegQry
WHERE rn = 1