I encountered a very strange problem: when I upgraded my SSIS package from SQL Integration Service 2005 to SQL Integration Service 2008, and tried to load flat files, the first row was always missing (With Column Names in First Row checked off and Header rows to skip as 0). I did lots of search and finally found out it is Microsoft SQL Server 2008 Integration Service issue. By applying the SQL Server 2008 Service Pack 3, the problem is gone.