Yes that is correct.. If you upload a DOS formatted text file in ASCII mode to a UNIX based server it will automatically convert the DOS text format to UNIX text format.
If you then download the same file using ASCII mode it will convert text file which is now UNIX formatted back to a DOS formatted text file.
If the file is at any point downloaded in BINARY mode then it gets remains UNIX formatted, depending on your text editor it may handle UNIX formatted text just fine, such as Ultra Edit or my personal favorite
NotePad++
Perhaps at some point the file format became messed up?
NotePad++ can convert the file from DOS to UNIX or UNIX to DOS. I would convert the file to DOS formatted and then upload it to your server and see if that resolve it.
If it doesn't resolve it, then I would re-evaluate whether or not the FTP server is actually using ASCII mode. There are some FTP servers that will use BINARY mode even when ASCII is selected.
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