I keep getting an error message when I run repair permissions that says, "Warning: SUID file “System/Library/CoreServices/RemoteManagement/ARDAgent.app/Contents/MacOS/ARDAgent” has been modified and will not be repaired." MacPro (early 2008)

Although it’s immensely popular, repairing permissions is pointless unless you have a specific indication of a permission error involving system files, which is rare, or a startup failure. It has traditionally spewed bogus warning messages that mean absolutely nothing.

The built-in help for Disk Utility reads in part:

If you see an alert or a message that says your permissions are set incorrectly, you can correct the disk’s permissions by clicking Repair Disk Permissions.

It’s justifiable, though rarely necessary, to repair permissions after running a third-party software installer, as defective installers have been known to damage the permissions of system files.

Mercifully, permission repair by the user will be abolished in OS X 10.11 ("El Capitan"), so people who now repair permissions can find a more productive use for their time.

<https://support.apple.com/HT203172>

As long as the report ends up with 'Permissions repair complete' then, as far as permissions go, you are fine. You can ignore the various statements in the report:

Permissions you can ignore on 10.5 onwards:

http://support.apple.com/kb/TS1448

Using 'should be -rw-r--r-- , they are lrw-r--r--' as an example, you will see the that the permissions are not changed, but the | indicates a different location. This is because an update to Leopard onwards changed the location of a number of system components.

Poster rccharles has provided this description of what it all means:

drwxrwxrwx

d = directory

r = read

w = write

x = executeable program

drwxrwxrwx

| | |

| | all other users not in first two types

| |

| group

|

owner

a little more info

Before the user had read & write. A member of the group had read.

After, only the user had read & write.