There are connection properties to define the transfer type and they most likely show up as a checkbox or drop-down with the words Bin/Binary and/or ASC/Ascii.
In Filezilla, for example, you can make this change in the preferences section as pictured below:
In the script that runs to download from the FTP site, execute the “binary” command. Alternatively, if you want to download the file as a text file, you can execute the “ascii” command.
For more information on ASC vs. BIN, please refer to http://serverfault.com/questions/110699/ascii-vs-binary-vs-auto/110781#110781