If you want to customize the ftp messages, you can edit ioFTPD's message files. They are located in ioFTPD\text\ftp\. You can add ANSI colour codes to these files.. but beware, not all ftp clients are compatible with these codes. FlashFXP is, I'm not sure for the others.
http://pueblo.sourceforge.net/doc/ma...lor_codes.html gives a list of the available codes.