On fresh FreePBX install it does not run a migration to take the old logger.conf and move it to the custom files.
Firstly logged via ssh and compared two files:
In my case they were identical.
So I did as following:
rm -rf /etc/asterisk/logger.conf ln -s /var/www/html/admin/modules/core/etc/logger.conf /etc/asterisk/logger.conf amportal reload
Thanx to the solution: corymar!