In SSIS, for fixed width flat file, new line character (CRLF) is NOT added at the end of the row. So when you run the package, all the rows are stored in one single line in the flat file.
You need to add additional column to the fixed width flat file and name it as CRLF (or name of your choice)
Here are two ways to add new line character after each row
1. New line character in resultset
Add new line character as a column in the SELECT statement.
SELECT CHAR(10) + CHAR(13) AS CRLF
Now you can use this column to map to an artificial CRLF column in the fixed width you created
2. New line character as derived column
Create a derived column called CRLF using the following expression and map it to the artificial CRLF column in the fixed width you created
And your problem is fixed.