Instead of having the server passively sit around and let other computers connect to it, it's going to actively request a random port number from clients to send data to. This is the difference between active and passive FTP in a nutshell. What does this mean? It means that instead of having to get through my firewall from the outside, the client's computer will have to accept a request from the server through it's own firewall. Normally, it will just be a pop-up from Windows Firewall wondering what you want to do with the incoming traffic (just hit "unblock".)
It's easy to set up your FTP client to use active FTP. Here, I've even screenshotted the button you need to hit, via the "Settings..." option in the "Edit" menu in the toolbar:

Hopefully that resolves any issues of file directories not showing up.
[Update] The server no longer requires active FTP to use. A client shouldn't need any changes to the settings to connect and use the server.