If the file is generated from windows and the transfer was in binary mode, the translation of CRLF characters is different on Unix systems.
You have to transfer it using ASCII mode.
If isn't possible to transfer it again from the original system, you can:
- transfer the file in any windows system using FTP binary mode
- transfer it again to Unix using FTP ASCII mode
This must correct the problem.
PS.: In unix are some commands that do this without using ftp, unfortunatly I havent this time access to unix system, search in unix for dos2unix command or something similar...