well i just did a clean install and i installed just the updates and repaired permissions. Then did the commands and repaird again and same thing.
I did each command and then repaired and found out that it is the monthly command that is causing the trouble. Here is the privileges that is messes up.
Repairing permissions for iBook HD
Determining correct file permissions.
Permissions differ on ./private/var/log/install.log, should be -rw-r--r-- , they are -rw-r-----
Owner and group corrected on ./private/var/log/install.log
Permissions corrected on ./private/var/log/install.log
Permissions differ on ./private/var/log/wtmp, should be -rw-r--r-- , they are -rw-r-----
Owner and group corrected on ./private/var/log/wtmp
Permissions corrected on ./private/var/log/wtmp
The privileges have been verified or repaired on the selected volume
Permissions repair complete