openssl s_client shows alert certificate unknown but all server certificates appear to be verified

I am troubleshooting errors establishing a secure connection to an EPP server. I issue the command below and see that all of the server certificates are verified, but still I get an error (highlighted in bold). Is there still a problem validating the server's certificates? If so, what could it be?

Edit: I snipped the "Acceptable client certificate CA names" because the spam detector didn't like them.

$ openssl s_client -connect otessl.verisign-grs.com:700 -key /home/ubuntu/foo.key -cert /home/ubuntu/foo.crt -CAfile /home/ubuntu/foo-cert-chain.pem  -CApath /etc/ssl/certs

CONNECTED(00000003)
depth=3 C = US, O = "VeriSign, Inc.", OU = Class 3 Public Primary Certification Authority
verify return:1
depth=2 C = US, O = "VeriSign, Inc.", OU = VeriSign Trust Network, OU = "(c) 2006 VeriSign, Inc. - For authorized use only", CN = VeriSign Class 3 Public Primary Certification Authority - G5
verify return:1
depth=1 C = US, O = "VeriSign, Inc.", OU = VeriSign Trust Network, OU = Terms of use at https://www.verisign.com/rpa (c)06, CN = VeriSign Class 3 Extended Validation SSL CA
verify return:1
depth=0 1.3.6.1.4.1.311.60.2.1.3 = US, 1.3.6.1.4.1.311.60.2.1.2 = Delaware, businessCategory = Private Organization, serialNumber = 2497886, C = US, postalCode = 20190, ST = Virginia, L = Reston, street = 12061 Bluemont Way, O = "Verisign, Inc", OU = Production Operations, CN = otessl.verisign-grs.com
verify return:1
<b>
140403406833312:error:14094416:SSL routines:SSL3_READ_BYTES:sslv3 alert certificate unknown:s3_pkt.c:1260:SSL alert number 46
140403406833312:error:140790E5:SSL routines:SSL23_WRITE:ssl handshake failure:s23_lib.c:177:
</b>
---
Certificate chain
 0 s:/1.3.6.1.4.1.311.60.2.1.3=US/1.3.6.1.4.1.311.60.2.1.2=Delaware/businessCategory=Private Organization/serialNumber=2497886/C=US/postalCode=20190/ST=Virginia/L=Reston/street=12061 Bluemont Way/O=Verisign, Inc/OU=Production Operations/CN=otessl.verisign-grs.com
   i:/C=US/O=VeriSign, Inc./OU=VeriSign Trust Network/OU=Terms of use at https://www.verisign.com/rpa (c)06/CN=VeriSign Class 3 Extended Validation SSL CA
 1 s:/C=US/O=VeriSign, Inc./OU=VeriSign Trust Network/OU=Terms of use at https://www.verisign.com/rpa (c)06/CN=VeriSign Class 3 Extended Validation SSL CA
   i:/C=US/O=VeriSign, Inc./OU=VeriSign Trust Network/OU=(c) 2006 VeriSign, Inc. - For authorized use only/CN=VeriSign Class 3 Public Primary Certification Authority - G5
 2 s:/C=US/O=VeriSign, Inc./OU=VeriSign Trust Network/OU=(c) 2006 VeriSign, Inc. - For authorized use only/CN=VeriSign Class 3 Public Primary Certification Authority - G5
   i:/C=US/O=VeriSign, Inc./OU=Class 3 Public Primary Certification Authority
---
Server certificate
-----BEGIN CERTIFICATE-----
*snipped*
-----END CERTIFICATE-----
subject=/1.3.6.1.4.1.311.60.2.1.3=US/1.3.6.1.4.1.311.60.2.1.2=Delaware/businessCategory=Private Organization/serialNumber=2497886/C=US/postalCode=20190/ST=Virginia/L=Reston/street=12061 Bluemont Way/O=Verisign, Inc/OU=Production Operations/CN=otessl.verisign-grs.com
issuer=/C=US/O=VeriSign, Inc./OU=VeriSign Trust Network/OU=Terms of use at https://www.verisign.com/rpa (c)06/CN=VeriSign Class 3 Extended Validation SSL CA
---
Acceptable client certificate CA names
*snipped - will post if needed*
---
SSL handshake has read 10228 bytes and written 4199 bytes
---
New, TLSv1/SSLv3, Cipher is RC4-MD5
Server public key is 2048 bit
Secure Renegotiation IS supported
Compression: NONE
Expansion: NONE
SSL-Session:
    Protocol  : TLSv1
    Cipher    : RC4-MD5
    Session-ID: 544D9C743C278DCE0AA4715E68CA7C7A3443F3596495EA3A27448B9F3E0AC575
    Session-ID-ctx: 
    Master-Key: 77E6E234FE7313C50C04B7C8F32B0D6C9B6520A114DA4253A97FF1C200544EBB21DBC2C7ECA45DF0546A27EFB466EF4F
    Key-Arg   : None
    PSK identity: None
    PSK identity hint: None
    SRP username: None
    Start Time: 1414372468
    Timeout   : 300 (sec)
    Verify return code: 0 (ok)
---

You get the error about certificate unknown from the server, so it refers to the validation of your client certificate on the server side and not to the (successful) validation of the servers certificate at the client side. That means the server does not like your client certificate.

Please check your client certificate against the list of acceptable CAs, make sure it is not revoked and maybe do a tcpdump/wireshark to verify, that it gets actually sent to the server. If this does not help you might check log files at the server side for signs what went wrong.

In my case

error:14094416:SSL routines:SSL3_READ_BYTES:sslv3 alert certificate unknown:s3_pkt.c:1260:SSL alert number 46

was solved by adding

ssl_verify_client_cert = yes

in /etc/dovecot/dovecot.conf.

I just experienced something similar.

You may have forgotten to install the CA Certificates.

If you're on ubuntu or debian: apt-get install ca-certificates