This has happened to me many times. I have a job that takes a flat file and imports it into sQL 2008 DB. From time to time, only half of a file will be imported, but no error is reported. If I reprocess the same exact file, it'll work OK, with all records imported completly. The file size doesn't seem to matter. It can happen to a file that has 5 rows, or a file that has half a million rows. I had the same issue when I was running DTS over SQL 2000 years ago.
Any idea?