You’ve stumbled across something that a lot of us deal with in the MS world when trying to accomplish this. From my personal experience with it I would do one of two things:
1)Consider using a standard FTP server with pgp encrypted files.
2)Consider using a third party product as you already have one of the better ones out there (IPSWITCH).
3)A potential solution might be to allow outside users a Web SSL VPN connection into a DMZ where all they can see is your FTP server and then pass files to it along a VPN tunnel. You’d need a cisco VPN 3005 or a newer ASA series firewall to do this though. Users would just hit a website, login to the SSL VPN and just click the object for the FTP server and pass a file along using the VPN tunnel and then sign out.
I’ve used the ipswitch ws_ftp pro client with good results with pgp encrypted and unencrypted files. The only problems I had with where when some boneheads used really old version of pgp which WS_FTP didn’t really like. Otherwise it worked well, esp with the automated scripting client it comes with and the auto-decryption of files ending in .pgp. That was great.