Loading facts happens twice when environmentpath is in the main section of puppet.conf

Did an upgrade from Puppet 3.4.3 to 3.6.1 (and also 3.6.0).
Now with a puppet run on the puppet master, facts are loaded twice, from modules directory and /var/lib/puppet;

Info: Retrieving plugin
Info: Loading facts in /etc/puppet/environments/tst/modules/netbackup/lib/facter/netbackup_agent_version.rb
Info: Loading facts in /etc/puppet/environments/tst/modules/netbackup/lib/facter/netbackup.rb
Info: Loading facts in /etc/puppet/environments/tst/modules/multipath/lib/facter/lvm2version.rb
Info: Loading facts in /etc/puppet/environments/tst/modules/multipath/lib/facter/multipathversion.rb
Info: Loading facts in /etc/puppet/environments/tst/modules/common/lib/facter/vendor.rb
Info: Loading facts in /etc/puppet/environments/tst/modules/common/lib/facter/runlevel.rb
Info: Loading facts in /etc/puppet/environments/tst/modules/common/lib/facter/ictro_status.rb
Info: Loading facts in /etc/puppet/environments/tst/modules/common/lib/facter/swap.rb
Info: Loading facts in /etc/puppet/environments/tst/modules/selinux/lib/facter/c_selinux.rb
Info: Loading facts in /etc/puppet/environments/tst/modules/vmware/lib/facter/vmware_tools_version.rb
Info: Loading facts in /etc/puppet/environments/tst/modules/vmware/lib/facter/vmware_esx_version.rb
Info: Loading facts in /etc/puppet/environments/tst/modules/ad/lib/facter/winbind.rb
Info: Loading facts in /etc/puppet/environments/tst/modules/stdlib/lib/facter/puppet_vardir.rb
Info: Loading facts in /etc/puppet/environments/tst/modules/stdlib/lib/facter/root_home.rb
Info: Loading facts in /etc/puppet/environments/tst/modules/stdlib/lib/facter/facter_dot_d.rb
Info: Loading facts in /etc/puppet/environments/tst/modules/stdlib/lib/facter/pe_version.rb
Info: Loading facts in /etc/puppet/environments/tst/modules/dell/lib/facter/omsa_version.rb
Info: Loading facts in /etc/puppet/environments/tst/modules/ovo/lib/facter/ovo_agent_version.rb
Info: Loading facts in /etc/puppet/environments/tst/modules/puppet/lib/facter/os_version.rb
Info: Loading facts in /etc/puppet/environments/tst/modules/ssh/lib/facter/sshdversion.rb
Info: Loading facts in /etc/puppet/environments/tst/modules/oracle/lib/facter/oracle.rb
Info: Loading facts in /etc/puppet/environments/tst/modules/iptables/lib/facter/iptables.rb
Info: Loading facts in /etc/puppet/environments/tst/modules/iptables/lib/facter/iptablesversion.rb
Info: Loading facts in /var/lib/puppet/lib/facter/multipathversion.rb
Info: Loading facts in /var/lib/puppet/lib/facter/ovo_agent_version.rb
Info: Loading facts in /var/lib/puppet/lib/facter/vmware_esx_version.rb
Info: Loading facts in /var/lib/puppet/lib/facter/vmware_tools_version.rb
Info: Loading facts in /var/lib/puppet/lib/facter/pe_version.rb
Info: Loading facts in /var/lib/puppet/lib/facter/lvm2version.rb
Info: Loading facts in /var/lib/puppet/lib/facter/netbackup.rb
Info: Loading facts in /var/lib/puppet/lib/facter/iptables.rb
Info: Loading facts in /var/lib/puppet/lib/facter/sshdversion.rb
Info: Loading facts in /var/lib/puppet/lib/facter/omsa_version.rb
Info: Loading facts in /var/lib/puppet/lib/facter/vendor.rb
Info: Loading facts in /var/lib/puppet/lib/facter/iptablesversion.rb
Info: Loading facts in /var/lib/puppet/lib/facter/oracle.rb
Info: Loading facts in /var/lib/puppet/lib/facter/facter_dot_d.rb
Info: Loading facts in /var/lib/puppet/lib/facter/os_version.rb
Info: Loading facts in /var/lib/puppet/lib/facter/netbackup_agent_version.rb
Info: Loading facts in /var/lib/puppet/lib/facter/ictro_status.rb
Info: Loading facts in /var/lib/puppet/lib/facter/c_selinux.rb
Info: Loading facts in /var/lib/puppet/lib/facter/root_home.rb
Info: Loading facts in /var/lib/puppet/lib/facter/puppet_vardir.rb
Info: Loading facts in /var/lib/puppet/lib/facter/winbind.rb
Info: Loading facts in /var/lib/puppet/lib/facter/swap.rb
Info: Loading facts in /var/lib/puppet/lib/facter/runlevel.rb

When I move the environmentpath from main section to master section in puppet.conf, facts are loaded normal again;
Info: Retrieving plugin
Info: Loading facts in /var/lib/puppet/lib/facter/multipathversion.rb
Info: Loading facts in /var/lib/puppet/lib/facter/ovo_agent_version.rb
Info: Loading facts in /var/lib/puppet/lib/facter/vmware_esx_version.rb
Info: Loading facts in /var/lib/puppet/lib/facter/vmware_tools_version.rb
Info: Loading facts in /var/lib/puppet/lib/facter/pe_version.rb
Info: Loading facts in /var/lib/puppet/lib/facter/lvm2version.rb
Info: Loading facts in /var/lib/puppet/lib/facter/netbackup.rb
Info: Loading facts in /var/lib/puppet/lib/facter/iptables.rb
Info: Loading facts in /var/lib/puppet/lib/facter/sshdversion.rb
Info: Loading facts in /var/lib/puppet/lib/facter/omsa_version.rb
Info: Loading facts in /var/lib/puppet/lib/facter/vendor.rb
Info: Loading facts in /var/lib/puppet/lib/facter/iptablesversion.rb
Info: Loading facts in /var/lib/puppet/lib/facter/oracle.rb
Info: Loading facts in /var/lib/puppet/lib/facter/facter_dot_d.rb
Info: Loading facts in /var/lib/puppet/lib/facter/os_version.rb
Info: Loading facts in /var/lib/puppet/lib/facter/netbackup_agent_version.rb
Info: Loading facts in /var/lib/puppet/lib/facter/ictro_status.rb
Info: Loading facts in /var/lib/puppet/lib/facter/c_selinux.rb
Info: Loading facts in /var/lib/puppet/lib/facter/root_home.rb
Info: Loading facts in /var/lib/puppet/lib/facter/puppet_vardir.rb
Info: Loading facts in /var/lib/puppet/lib/facter/winbind.rb
Info: Loading facts in /var/lib/puppet/lib/facter/swap.rb
Info: Loading facts in /var/lib/puppet/lib/facter/runlevel.rb