here's a test scenario in a ready to use format, returning the expected(?) result.

So, I don't see anything wrong with the code.

declare @tbl table(vndnbr int, InvNbr int, InvAmt numeric(18,6),ChkNbr int)

insert into @tbl

SELECT 687840 , 423099 , -23.000000,1 union all

SELECT 687840 , 423099 , -23.000000,2 union all

SELECT 687840 , 423099 , 23.000000,3 union all

SELECT 603031 , 106541 , -781.410000,1 union all

SELECT 603031 , 106541 , -781.410000,1 union all

SELECT 603031 , 106541 , 781.410000,1

Select *

FROM (

Select S1.*, S2.Cnt , rn = ROW_NUMBER() OVER (PARTITION BY InvAmt_Sum ORDER BY ChkNbr DESC)

From @tbl as S1

Inner join ( Select VndNbr, InvNbr, Sum(InvAmt) as InvAmt_Sum, Count(*) as Cnt

From @tbl

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