Problem still persisted in 3.9.1
Here is the debug log:
INFO [SCPClient] 24 Oct 2011 10:47:00.321 : SCPClient settings validated.
DEBUG [SCPClient] 24 Oct 2011 10:47:00.321 : Connecting to sa1-cst548-01:22
DEBUG [StreamSocketFactory] 24 Oct 2011 10:47:00.321 : Connecting to sa1-cst548-01:22 via standard socket
INFO [TransportProtocolCommon] 24 Oct 2011 10:47:00.321 : Timeout=60000
DEBUG [TransportProtocolCommon] 24 Oct 2011 10:47:00.321 : Starting transport protocol
DEBUG [TransportProtocolCommon] 24 Oct 2011 10:47:00.322 : Registering transport protocol messages with inputstream
DEBUG [TransportProtocolCommon] 24 Oct 2011 10:47:00.322 : Negotiating protocol version
DEBUG [TransportProtocolCommon] 24 Oct 2011 10:47:00.322 : Local identification: SSH-2.0-edtFTPjPRO-3.9.1
INFO [TransportProtocolCommon] 24 Oct 2011 10:47:00.322 : Wait for state update timeout=60000
DEBUG [TransportProtocolCommon] 24 Oct 2011 10:47:00.328 : Read: 'SSH-2.0-WeOnlyDo-wodFTPD 2.3.6.165
'
DEBUG [TransportProtocolCommon] 24 Oct 2011 10:47:00.328 : EOL is guessed at CR+LF
DEBUG [TransportProtocolCommon] 24 Oct 2011 10:47:00.328 : Remote identification: 'SSH-2.0-WeOnlyDo-wodFTPD 2.3.6.165'
DEBUG [TransportProtocolCommon] 24 Oct 2011 10:47:00.328 : Protocol negotiation complete
DEBUG [TransportProtocolCommon] 24 Oct 2011 10:47:00.328 : Name=SSH_MSG_KEX_INIT,MessageId=20
Supported Kex diffie-hellman-group1-sha1,diffie-hellman-group-exchange-sha1
Supported Public Keys ssh-dss,ssh-rsa
Supported Encryption Client->Server blowfish-cbc,aes128-cbc,3des-cbc,aes192-cbc,aes256-cbc,arcfour
Supported Encryption Server->Client blowfish-cbc,aes128-cbc,3des-cbc,aes192-cbc,aes256-cbc,arcfour
Supported Mac Client->Server hmac-sha1,hmac-md5-96,hmac-sha1-96,hmac-md5
Supported Mac Server->Client hmac-sha1,hmac-md5-96,hmac-sha1-96,hmac-md5
Supported Compression Client->Server none,zlib
Supported Compression Server->Client none,zlib
Supported Languages Client->Server
Supported Languages Server->Client
First Kex Packet Follows [FALSE]
DEBUG [TransportProtocolCommon] 24 Oct 2011 10:47:00.328 : Sending SSH_MSG_KEX_INIT
INFO [TransportProtocolCommon] 24 Oct 2011 10:47:00.328 : Wait for state update timeout=60000
DEBUG [SshMsgKexInit] 24 Oct 2011 10:47:00.328 : Packetlength=428, Paddinglength=8
DEBUG [TransportProtocolCommon] 24 Oct 2011 10:47:00.328 : Received registered message: SSH_MSG_KEX_INIT
DEBUG [TransportProtocolCommon] 24 Oct 2011 10:47:00.328 : Received Name=SSH_MSG_KEX_INIT,MessageId=20
Supported Kex diffie-hellman-group1-sha1
Supported Public Keys ssh-rsa
Supported Encryption Client->Server aes128-cbc,3des-cbc,blowfish-cbc,aes192-cbc,aes256-cbc,rijndael128-cbc,rijndael192-cbc,rijndael256-cbc,rijndael-cbc@lysator.liu.se
Supported Encryption Server->Client aes128-cbc,3des-cbc,blowfish-cbc,aes192-cbc,aes256-cbc,rijndael128-cbc,rijndael192-cbc,rijndael256-cbc,rijndael-cbc@lysator.liu.se
Supported Mac Client->Server hmac-sha1,hmac-md5,none
Supported Mac Server->Client hmac-sha1,hmac-md5,none
Supported Compression Client->Server zlib,none
Supported Compression Server->Client zlib,none
Supported Languages Client->Server
Supported Languages Server->Client
First Kex Packet Follows [FALSE]
DEBUG [TransportProtocolCommon] 24 Oct 2011 10:47:00.328 : Starting key exchange
DEBUG [TransportProtocolCommon] 24 Oct 2011 10:47:00.328 : Determine Algorithm
DEBUG [TransportProtocolCommon] 24 Oct 2011 10:47:00.328 : Client Algorithms: [diffie-hellman-group1-sha1, diffie-hellman-group-exchange-sha1]
DEBUG [TransportProtocolCommon] 24 Oct 2011 10:47:00.328 : Server Algorithms: [diffie-hellman-group1-sha1]
DEBUG [TransportProtocolCommon] 24 Oct 2011 10:47:00.328 : Returning diffie-hellman-group1-sha1
DEBUG [TransportProtocolCommon] 24 Oct 2011 10:47:00.328 : Key exchange algorithm: diffie-hellman-group1-sha1
INFO [DhGroup1Sha1] 24 Oct 2011 10:47:00.328 : Starting client side key exchange.
WARN [TransportProtocolCommon] 24 Oct 2011 10:47:00.328 : The Transport Protocol thread failed: com.enterprisedt.cryptix.provider.elgamal.BaseElGamalKeyPairGenerator
DEBUG [TransportProtocolCommon] 24 Oct 2011 10:47:00.328 : stop() called
INFO [TransportProtocolCommon] 24 Oct 2011 10:47:00.328 : The Transport Protocol has been stopped