Since many fixed length text files come with a CR LF pair at the end of records, maybe there are CR LF problems?
I.e. your ouput file has only LFs (ala Unix, output by PHP and incompatible with DOS/Windows loaders), MS-DOS editor opens it anyway (it's sort of smart!) and saves using CR + LF a la DOS.
To be more sure, open the file in Notepad and then in Wordpad.
If in Notepad the formatting at EOLs is screwed up and in Wordpad not (BTW Wordpad works the same as MS-DOS editor in putting CR+LF in LF only files...), then that is the problem.
To solve it fast, simply put a CR (0x0D) at the end of the rows.