We currently use a SQC (Statiscal Quality Control) program through the use of Pareto Charts to track scrap operation by operation-and a lot of other details.
 
It would be good if DBA could track either way. Perhaps it could be through Enter Finished Production with a sequence number that may or may not be used.  It does appear that one of the drawbacks in current DBA is that scrap does not reduce the parts available when running MRP.  Not sure how it effects such thing as availability in inventory module-I haven't tracked an item through to that point.
 
Something like this would permit the elimination of one more separate programs, providing appropriate reports could be generated, including the simple calculation of % of scrap