I think the odd behaviour you are seeing will disappear if you use a having clause rather than a where clause for the sum criteria. I find that where clauses don't do well with criteria that require an aggregate.

Try this:

SELECT ;
		APTRXFIL.VOUCHER_NO, ;
		APTRXFIL.INV_AMT, ;
		SUM(APTRXDST.DST_AMT) AS DST_AMT ;
	FROM ;
		APTRXFIL, ;
		APTRXDST ;
	WHERE ;
		APTRXFIL.VOUCHER_NO = APTRXDST.VOUCHER_NO ;
        HAVING ;
		APTRXFIL.INV_AMT <> SUM(APTRXDST.DST_AMT) ;
	GROUP BY ;
		APTRXFIL.VOUCHER_NO, ;
		APTRXFIL.INV_AMT ;
	INTO CURSOR tmpAPTransactions