To fix this some chmod commands need to be executed in the terminal.
Essentially open up a terminal and do the following:
cd / ls -le
look at the Applications and Library folders in the listing and you should see they have specific ACLs. On one of my machines the Applications folder had 2 and the Library had one. On the other both had just one.
to remove these ACLs do the following:
sudo chmod -a# 0 Applications
sudo chmod -a# 0 Library
#################################
Ok another easy way to do this is:
chmod -R -N <folder to remove ACL from>
ACL missing on "System/Library/User Template/English.lproj/Pictures/iChat Icons/Flags".
I downloaded Mac Pilot and went to -->Tools/Wipe Access Control list Data---> navigated to here--->/Library/Application Support/Apple/iChat Icons and now I have a clean bill of health in Disk Utility's permissions repair.