I know this question has been sort of answered but not properly in my opinion.
There should be no permissions to repair once they have been repaired.
There should also be no permissions that can't be fixed especailly by Apple.
Many computers have seen this:
"System/Library/CoreServices/RemoteManagement/ARDAgent.app/Contents/MacOS/ARDAge nt" has been modified and will not be repaired."
To me this is not normal even though Apple may say it is.
Not all computers have this so why do some other computers show this problem?
I have fixed this on my computers as I can't stand to have things like this show up when they shouldn't.
I replaced the problematic ArdAgent by using a copy from another computer that did not have that warning.
Once, replaced, I got the message in Disk Utility when I repaired the permissions with this new one:
Permissions differ for:
System/Library/CoreServices/RemoteManagement/ARDAgent.app/Contents/MacOS/ARDAgen t
should be "0" instead of 501 (or something like this)
Then it states those permissions were repaired.
Now I no longer get that stupid warning about the ARDAgent.
For those of you that want to get rid of that warning, try using a copy from another computer running the same system.
Worked for me.
I also repaired a few other permissions that always kept coming back even though Disk Utility said they were repaired.
Hogwash.
If it was repaired then the same exact ones wouldn't be coming back everytime you repair permissions.
In my mind, there should be no permissions to repair once they have been repaired.
Otherwise, they were not fixed or repaired in the first place.
I now no longer have any permissions to repair unless I may install something new that might need repair.
Good luck with your mileage.
This is how Disk Utility should look like without any permissions to repair once you have repaired them one time, and one time, only.
Clean bill of health.