Earlier this year a security update to Windows Server changed the way cipher negotiation for FTP with TLS works. The change was made for an HTTPS vulnerability, but it affected FTP TLS also.
After that, clients like WinSCP and Filezilla and clients that use the GNU SSL library stopped working with Windows Server IIS FTP+TLS. WinSCP will connect and display directory listings, but file transfers abort with the message:
"Copying files to remote side failed. The supplied message is incomplete. The signature was not verified."
Users have reported this problem but AFAIK the incompatibility is still not fixed. The client/library writers blame Microsoft for breaking TLS. Microsoft, as per normal with standards, either doesn't care or will take 5-10 years to get around to fix. A client workaround would be nice, but the Filezilla maintainer has had multiple tantrums over it in the forums :-(
The good news is WinSCP 5.2.4 beta enables a workaround. The new TLS/SSL site options let you set the maximum version to 'TLS 1.0', and this acts as a workaround for the problem. WinSCP can be used with Windows Server IIS for FTP + TLS again!!
This would be good to document somewhere.