"Unix, Windows and Mac systems all have their own newline characters. When transferring files as ASCII, most FTP clients convert these newlines if applicable. So: one could set up Filezilla to handle text files as ASCII.
However, it seems that the newlines in the files on the server do not match the operating system of that server. Hence, when using automatic conversion, things get messed up. So, like @Manni suggested: you need to ensure all files are handled as ""binary"", not as ASCII.
(Note that many other files, such as program files, Word documents, music and images always need to be transferred as ""binary"", to ensure no automatic conversion is done.)"