Hi Radek,
are you using any configs for PolicyKit?
If not this would be one way of quickly fixing the problem.
If you are using some custom policykit config please attach it here, so we could help you more.
this file /usr/local/etc/PolicyKit/PolicyKit.conf.sample includes this part:
<match user="root">
<return result="yes"/>
</match>
copy the file to /usr/local/etc/PolicyKit/PolicyKit.conf
and add your username to the config.
<match user="root|radek">
<return result="yes"/>
</match>
This would be a very basic config.