I got the same error now in 5.0.1353.0. Connecting to the server has always worked fine (and still works fine over putty), but fails with SmartFTP.
[18:28:43] SmartFTP v5.0.1353.0
[18:28:43] Resolving host name "xyz"
[18:28:43] Connecting to x.x.x.x Port: 22
[18:28:44] Connected to ....
[18:28:44] SSH protocol version reply. Client Id: SSH-2.0-SmartFTP
[18:28:44] SSH-2.0-OpenSSH_6.5
[18:28:44] Starting SSH session. Remote Id: "SSH-2.0-OpenSSH_6.5"
[18:28:44] Server Algorithm Suite
Key Exchange: curve25519-sha256@libssh.org,ecdh-sha2-nistp256,ecdh-sha2-nistp384,ecdh-sha2-nistp521,diffie-hellman-group-exchange-sha256,diffie-hellman-group-exchange-sha1,diffie-hellman-group14-sha1,diffie-hellman-group1-sha1
Server Host Key: ssh-rsa,ssh-dss,ecdsa-sha2-nistp256,ssh-ed25519
Client to Server Encryption: aes128-ctr,aes192-ctr,aes256-ctr,arcfour256,arcfour128,aes128-gcm@openssh.com,aes256-gcm@openssh.com,chacha20-poly1305@openssh.com,aes128-cbc,3des-cbc,blowfish-cbc,cast128-cbc,aes192-cbc,aes256-cbc,arcfour,rijndael-cbc@lysator.liu.se
Server to Client Encryption: aes128-ctr,aes192-ctr,aes256-ctr,arcfour256,arcfour128,aes128-gcm@openssh.com,aes256-gcm@openssh.com,chacha20-poly1305@openssh.com,aes128-cbc,3des-cbc,blowfish-cbc,cast128-cbc,aes192-cbc,aes256-cbc,arcfour,rijndael-cbc@lysator.liu.se
Client to Server HMAC: hmac-md5-etm@openssh.com,hmac-sha1-etm@openssh.com,umac-64-etm@openssh.com,umac-128-etm@openssh.com,hmac-sha2-256-etm@openssh.com,hmac-sha2-512-etm@openssh.com,hmac-ripemd160-etm@openssh.com,hmac-sha1-96-etm@openssh.com,hmac-md5-96-etm@openssh.com,hmac-md5,hmac-sha1,umac-64@openssh.com,umac-128@openssh.com,hmac-sha2-256,hmac-sha2-512,hmac-ripemd160,hmac-ripemd160@openssh.com,hmac-sha1-96,hmac-md5-96
Server to Client HMAC: hmac-md5-etm@openssh.com,hmac-sha1-etm@openssh.com,umac-64-etm@openssh.com,umac-128-etm@openssh.com,hmac-sha2-256-etm@openssh.com,hmac-sha2-512-etm@openssh.com,hmac-ripemd160-etm@openssh.com,hmac-sha1-96-etm@openssh.com,hmac-md5-96-etm@openssh.com,hmac-md5,hmac-sha1,umac-64@openssh.com,umac-128@openssh.com,hmac-sha2-256,hmac-sha2-512,hmac-ripemd160,hmac-ripemd160@openssh.com,hmac-sha1-96,hmac-md5-96
Client to Server Compression: none,zlib@openssh.com
Server to Client Compression: none,zlib@openssh.com
[18:28:44] Selected Algorithm Suite
Key Exchange: curve25519-sha256@libssh.org
Server Host Key: ecdsa-sha2-nistp256
Client to Server Encryption: aes128-gcm@openssh.com
Server to Client Encryption: aes128-gcm@openssh.com
Client to Server HMAC: none
Server to Client HMAC: none
Client to Server Compression: zlib@openssh.com
Server to Client Compression: zlib@openssh.com
[18:28:44] Client Algorithm Suite
Key Exchange: curve25519-sha256@libssh.org,ecdh-sha2-nistp256,ecdh-sha2-nistp384,ecdh-sha2-nistp521,diffie-hellman-group-exchange-sha256,diffie-hellman-group-exchange-sha1,diffie-hellman-group1-sha1,diffie-hellman-group14-sha1,rsa1024-sha1
Server Host Key: ecdsa-sha2-nistp256,ecdsa-sha2-nistp384,ecdsa-sha2-nistp521,x509v3-sign-rsa-sha1,x509v3-sign-dss-sha1,ssh-rsa,ssh-dss
Client to Server Encryption: aes128-gcm@openssh.com,aes256-gcm@openssh.com,aes256-ctr,aes256-cbc,rijndael256-cbc,rijndael-cbc@lysator.liu.se,aes192-ctr,aes192-cbc,rijndael192-cbc,aes128-ctr,aes128-cbc,rijndael128-cbc,3des-cbc,blowfish-cbc,cast128-cbc
Server to Client Encryption: aes128-gcm@openssh.com,aes256-gcm@openssh.com,aes256-ctr,aes256-cbc,rijndael256-cbc,rijndael-cbc@lysator.liu.se,aes192-ctr,aes192-cbc,rijndael192-cbc,aes128-ctr,aes128-cbc,rijndael128-cbc,3des-cbc,blowfish-cbc,cast128-cbc
Client to Server HMAC: hmac-sha2-512,hmac-sha2-256,hmac-sha1,hmac-md5,umac-64@openssh.com,hmac-ripemd160
Server to Client HMAC: hmac-sha2-512,hmac-sha2-256,hmac-sha1,hmac-md5,umac-64@openssh.com,hmac-ripemd160
Client to Server Compression: zlib@openssh.com,zlib,none
Server to Client Compression: zlib@openssh.com,zlib,none
[18:28:44] Key Exchange Algorithm: curve25519-sha256@libssh.org
[18:28:44] Server closed connection
[18:28:44] Connect failed. Error=0x80043112
[18:28:44] Waiting to retry (30s)...
Strange thing is that it does something with certificates here even though I only activated "passworc" as authentication mechanism and using keys would not work because I have none.