Started off with a clean slate.
puppetmasterd --mkusers

[root@test1 manifests]# ls -ld /var/puppet
drwxr-xr-x 10 root root 4096 Mar 17 15:04 /var/puppet
[root@test1 manifests]# ls -l /var/puppet/
total 32
drwxr-x--- 2 puppet puppet 4096 Mar 17 15:04 bucket
drwxr-x--- 2 root   root   4096 Mar 17 15:04 clientbucket
drwxr-xr-x 2 root   root   4096 Mar 17 15:04 lib
drwxr-x--- 2 puppet puppet 4096 Mar 17 15:04 log
drwxr-x--- 2 puppet puppet 4096 Mar 17 15:04 reports
drwxr-xr-x 2 puppet puppet 4096 Mar 17 15:04 rrd
drwxrwxrwt 2 puppet puppet 4096 Mar 17 15:08 run
drwxr-xr-t 2 root   root   4096 Mar 17 15:04 state

Logs...

Mar 17 15:07:10 test1 puppetmasterd[2344]: (/Settings[top]/Settings[yaml]/File[/var/puppet/yaml]/ensure) change from absent to directory failed: Could not set directory on ensure: Permission denied - /var/puppet/yaml

[root@test1 manifests]# chown puppet /var/puppet
[root@test1 manifests]# puppetmasterd
[root@test1 manifests]# ls -l /var/puppet/
total 36
drwxr-x--- 2 puppet puppet 4096 Mar 17 15:04 bucket
drwxr-x--- 2 root   root   4096 Mar 17 15:04 clientbucket
drwxr-xr-x 2 root   root   4096 Mar 17 15:04 lib
drwxr-x--- 2 puppet puppet 4096 Mar 17 15:04 log
drwxr-x--- 2 puppet puppet 4096 Mar 17 15:04 reports
drwxr-xr-x 2 puppet puppet 4096 Mar 17 15:04 rrd
drwxrwxrwt 2 puppet puppet 4096 Mar 17 15:09 run
drwxr-xr-t 2 root   root   4096 Mar 17 15:04 state
drwxr-x--- 3 puppet puppet 4096 Mar 17 15:09 yaml