FTP isn't a supported use of Windows Home Server, so beyond telling you to open the correct ports in your router's firewall (port 21 is the control port, then usually port 20 is the standard data port), there isn't a lot of assistance that you'll get here. However, it's likely that the FTP software you're using makes use of active, passive, or extended passive mode for file transfers. Those dynamically allocated ports may still be blocked by your server's firewall, your router's firewall, or both.
I would suggest you try contacting the software vendor for assistance.
I'm not on the WHS team, I just post a lot. :)