[Puppet Agent] Agent cannot resolve ssldir correctly

My problem is very similar to this issue, however my problem does not go away when I delete /var/lib/puppet/ssl directory.

So, I have a Puppet Master that is also configured as its agent. Since I prefer a bit different directory structure that currently Puppet uses (I prefer the previous convention), I overridden some paths in the config:

[main]

logdir = /var/log/puppet

vardir = /var/lib/puppet

ssldir = /var/lib/puppet/ssl

rundir = /var/run/puppet

factpath = $vardir/lib/facter

confdir = /etc/puppet

codedir = /etc/puppet

[agent]

server = central.int.example.com

[master]

daemonize = false

ssl_client_header = SSL_CLIENT_S_DN

ssl_client_verify_header = SSL_CLIENT_VERIFY

dns_alt_names = puppet,puppet.szervernet.hu

When I start agent, it does not pick up the overridden ssldir, nor the server directive under its own section.

root@central:/etc/puppet# puppet agent --configprint ssldir

/etc/puppetlabs/puppet/ssl

root@central:/etc/puppet#

I deleted /var/lib/puppet/ssl twice in a row and did not helped. But regardless of this, I think agent have to pick up overridden settings. Even if it's not follows any standards. If master can use these settings, agent have to do so.