Issue #19680 has been updated by Jason Barnett.

I ran into this error when I copied over the ssl directory from a puppet master 
v2.7.20. I then started to start from a clean slate and I still ran into some 
weird issues... Running through the commands below, I can repeat the problem. 
"puppet ca list --all" won't work until I run "puppet cert list --all"

[22:18:26 CDT] root@puppet001 [/etc/puppet]# puppet ca generate puppetca 
--dns-alt-names puppetca.domain.com,mypuppettest
Notice: Signed certificate request for ca
Notice: Rebuilding inventory file
Notice: puppetca has a waiting certificate request
Notice: Signed certificate request for puppetca
Notice: Removing file Puppet::SSL::CertificateRequest puppetca at 
'/etc/puppet/ssl/ca/requests/puppetca.pem'
Notice: Removing file Puppet::SSL::CertificateRequest puppetca at 
'/etc/puppet/ssl/certificate_requests/puppetca.pem'
"-----BEGIN 
CERTIFICATE-----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\nuwIDAQABo4HTMIHQMDcGCWCGSAGG+EIBDQQq
 
FihQdXBwZXQgUnVieS9PcGVuU1NM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\nR66gBhdz2UTylK0pkmHuZnK+YvoKpecBpUn
 b9+qIEWw=\n-----END CERTIFICATE-----\n"
[22:18:49 CDT] root@puppet001 [/etc/puppet]# puppet ca list --all
Error: system lib
Error: Try 'puppet help ca list' for usage
[22:18:54 CDT] root@puppet001 [/etc/puppet]# puppet cert list --all
Notice: Signed certificate request for ca
+ "puppetca" (SHA256) 
09:3D:1E:E4:2E:44:95:2F:3A:23:64:02:2C:0E:0E:CB:F3:A6:1B:EF:12:FE:FC:4D:55:A8:3E:6B:D7:17:00:EB
 (alt names: "DNS:mypuppettest", "DNS:puppetca", "DNS:puppetca.domain.com")
[22:19:00 CDT] root@puppet001 [/etc/puppet]# puppet ca list --all
+ puppetca  (SHA256) 
09:3D:1E:E4:2E:44:95:2F:3A:23:64:02:2C:0E:0E:CB:F3:A6:1B:EF:12:FE:FC:4D:55:A8:3E:6B:D7:17:00:EB
[22:19:03 CDT] root@puppet001 [/etc/puppet]# puppet --version
3.2.3

----------------------------------------
Bug #19680: puppet ca list --all fails with "Error: The certificate retrieved 
from the master does not match the agent's private key."
https://projects.puppetlabs.com/issues/19680#change-96217

* Author: Deven Phillips
* Status: Investigating
* Priority: Normal
* Assignee: Andrew Parker
* Category: SSL
* Target version: 
* Affected Puppet version: 3.1.0
* Keywords: ca cert certificate private_key mismatch
* Branch: 
----------------------------------------
On my puppetmaster server (using Apache, PhusionPassenger, puppet 3.1.0-1 on 
Debian Squeeze), attempting to run "puppet ca list --all" fails with:

    Error: The certificate retrieved from the master does not match the agent's 
private key.
    Certificate fingerprint: [[REDACTED]]
    To fix this, remove the certificate from both the master and the agent and 
then start a puppet run, which will automatically regenerate a certficate.
    On the master:
    puppet cert clean [[REDACTED]]
    On the agent:
    rm -f /etc/puppet/ssl/certs/[[REDACTED]].pem
    puppet agent -t
    Error: Try 'puppet help ca list' for usage

I have used "openssl x509 -in /path/to/cert.pem -fingerprint -md5 -nooout" to 
check the fingerprints on all certs and they DO match.

Additionally, running "puppet cert list --all" works without issue.


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