Safesquid blocks access to my works ftp site. I tried configuring it in passive mode, that didn't work. I tried putting the user name and password in the ftp section of safesquid.cfg, that didn't work. When you go to the site it never even asks for the username or password, it just states that access is denied. When in passive mode, when I go to the site, it still doesn't ask for the user or pass, it just displays a blank page, with a light blue header at the top, with the options delete, rename, mkdir, rmdir, regexp match, raw command, and argument, which is not what the site that is supposed to be displayed.

Anyone have any ideas on how to fix this issue?

Use an FTP client that allows you to define a proxy.
You can control access to FTP from the SafeSquid Interface.