Mystery solved: I was not getting an accurate row count using

select APPNUMBER = COUNT(*) from SCORECARDAPP_TEST _new

When querying the dmv I was able to get the exact count as the flat file.

SELECT SUM (row_count)

FROM sys.dm_db_partition_stats

WHERE object_id=OBJECT_ID('SCORECARDAPP_TEST_new')

AND (index_id=0 or index_id=1);

Thanks Everyone!

Doug