When you say the order was changed, did you mean that a select from the table returns the rows in a different sequence than they were in the flatfile? If so, the answer is simply that a SQL Server table has NO GUARANTEE OF ORDER for a query without using the ORDER BY clause. Although, especially with smaller tables, you may often see data returned in the same sequences as it was inserted, there is no implicit order.
If you want the data returned from SQL Server in a particular order, specify it with ORDER BY.