I'm using logwatch a RHEL6 server. When starting logwatch manually as root every works perfect.
------------- Directory Sizes ---------------
Size Location (GB)
207M /var/log
1.7G /usr
------------- Directory Sizes ---------------
------------- Home Directory Sizes ---------------
Size Location (MB)
488K /home/userA
116K /home/userB
92K /home/userC
------------- Home Directory Sizes ---------------

If running logwatch via cron.daily I receive these results:

------------- Directory Sizes ---------------
Size Location (GB)
du: cannot read directory `/var/log/audit': Permission denied
488M /var/log
du: cannot read directory `/usr/lib64/httpd': Permission denied
du: cannot read directory `/usr/lib64/games': Permission denied
du: cannot read directory `/usr/lib/games': Permission denied
du: cannot read directory `/usr/share/cracklib': Permission denied
du: cannot read directory `/usr/share/man': Permission denied
du: cannot read directory `/usr/share/X11/fonts': Permission denied
du: cannot read directory `/usr/share/fonts': Permission denied
du: cannot read directory `/usr/share/hwdata': Permission denied
du: cannot read directory `/usr/local/share/man': Permission denied
1.6G /usr
------------- Directory Sizes ---------------
------------- Home Directory Sizes ---------------
Size Location (MB)
du: cannot access `/home/*': No such file or directory
------------- Home Directory Sizes ---------------

I checked the permissions and they look ok. I also compared configs and permissions with other servers having logwatch working and they are pretty much the same.

Any ideas?

Could you post the cron.daily config?

What do you mean by cron.daily config?
The 0logwatch config?

The issue is fixed.
It was an selinux issue