After editing OpenSSH.pm to not disable publickey and not getting anywhere while being able to run same ssh command manually I got stuck. The problem is public key authentication (key is coming from ssh-agent, NOT the local file) to the gateway host. Here is what happens with one called from perl :

# call args: ['ssh','-o','CheckHostIP no','-o','HashKnownHosts no','-o
+','StrictHostKeyChecking no','-o','VerifyHostKeyDNS no','-o','UserKno
+wnHostsFile /dev/null','-o','HostbasedAuthentication no','-o','Challe
+ngeResponseAuthentication no','-o','RhostsRSAAuthentication no','-o',
+'GSSAPIAuthentication no','-o','ProxyCommand=ssh -o "PasswordAuthenti
+cation no" -o "GSSAPIAuthentication no" -vvv -k root@192.168.1.1 nc %
+h 22','-o','PasswordAuthentication yes','-o','PubkeyAuthentication ye
+s','-o','ServerAliveInterval=30','-x2MN','-o','NumberOfPasswordPrompt
+s=1','-o','PreferredAuthentications=publickey,keyboard-interactive,pa
+ssword','-S','/root/.libnet-openssh-perl/root-10.20.30.40-16309-99228
+','-l','root','10.20.30.40','--']
[download]

Output from perl:

debug1: Authentications that can continue: publickey,gssapi-with-mic,p
+assword
debug3: start over, passed a different list publickey,gssapi-with-mic,
+password
debug3: preferred publickey,keyboard-interactive
debug3: authmethod_lookup publickey
debug3: remaining preferred: keyboard-interactive
debug3: authmethod_is_enabled publickey
debug1: Next authentication method: publickey
debug1: Trying private key: /root/.ssh/id_rsa
debug3: no such identity: /root/.ssh/id_rsa
debug1: Trying private key: /root/.ssh/id_dsa
debug3: no such identity: /root/.ssh/id_dsa
debug2: we did not send a packet, disable method
debug1: No more authentication methods to try.
Permission denied (publickey,gssapi-with-mic,password).
[download]

And this one is manual :

ssh -o "CheckHostIP no" -o "HashKnownHosts no" -o "StrictHostKeyChecki
+ng no" -o "VerifyHostKeyDNS no" -o "UserKnownHostsFile /dev/null" -o 
+"PasswordAuthentication yes" -o "PubkeyAuthentication yes" -o "ProxyC
+ommand=ssh -vvv root@192.168.1.1 nc %h 22" -o "ServerAliveInterval=30
+" -x2MN -o "NumberOfPasswordPrompts=1" -o "PreferredAuthentications=p
+ublickey,keyboard-interactive,password" -S /tmp/zzz -l root 10.20.30.
+40
[download]

Output:

debug3: remaining preferred: publickey,keyboard-interactive,password
debug3: authmethod_lookup publickey
debug3: remaining preferred: keyboard-interactive,password
debug3: authmethod_is_enabled publickey
debug1: Next authentication method: publickey
debug1: Offering DSA public key: /HOME/MY_KEY.DSA
debug3: send_pubkey_test
debug2: we sent a publickey packet, wait for reply
debug1: Server accepts key: pkalg ssh-dss blen 432
[download]

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