Ok I understand everything in that article you posted. I've been aware of those changes from the updates fom 10.4.2 up to 10.4.7.
But, that is not what I'm talking about; let me re-explain the post you replied to.
When I used the Disk Utility, on the start up disk, to repair Disk Permissions, it made many "corrections." I then ran it again a secon time to make sure it was cleared up-which it was.
A while after, an hour later I was updating my Istat Pro Widget. I decided to repair permissions after the update, which is what I always do after installing, or updating an application. And, when I ran disk utility on the HD, I got a whole bunch of "corrections" that needed repair; which all looked very siimilar to the permissions that needed "corrections."
Im not talking about "we are using specail permissions"
And, I bet my money on it , if I was to re-boot using my start up disk it would then repair all the same permissions again.
I have no clue, other than the fact that I am using a 10.4.2 start up disk, to repair a 10.4.7 OS.