Ok, so I run my own servers, and included in which is an FTP Server. I updated recently and they decided they would no longer support the "SITE" or "CHMOD" directives. I want to know if there is a way to set file permissions for files on my FTP server on my Windows machine without logging onto the server with an ftp client and using the CHMOD command. I need to be able to set files that same access as CHMOD 777 (rwx-rwx-rwx).

You can CHMOD via SSH...

No, see I run my servers off my own machine, and everything is run off my computer which is Windows XP SP1. I need to be able to alter file permissions from my side (server) because I can no longer altar them from my side (user).

The servers are on a Widnows machine, hence I need an app or method to run on a windows machine to change ftp file permissions.

AFAIK SSH is *nix only.

http://www.webmasterworld.com/forum92/1888.htm

Try that, it's another thread I found on google with a similar issue.  I hope it helps.