I think SUNIQUE is a z/OS dependent FTP command. If so, it is not surprising to see issues with IIS 6 FTP.
http://publib.boulder.ibm.com/infocenter/zos/v1r10/index.jsp?topic=/com.ibm.zos.r10.halu001/sunique.htm
http://publib.boulder.ibm.com/infocenter/zvm/v5r3/index.jsp?topic=/com.ibm.zvm.v53.kijl0/sunique.htm
You may consult AS/400 vendor to see if there is a way to configure its FTP client to work with IIS 6 FTP.
Also check this old thread,
http://www.tech-archive.net/Archive/Internet-Server/microsoft.public.inetserver.iis.ftp/2006-06/msg00034.html