Q: after running permissions repair i get the folling msg.  Warning: SUID file “System/Library/CoreServices/RemoteManagement/ARDAgent.app/Contents/MacOS/ARDAg ent” has been modified and will not be repaired.

That's a normal occurrence ignore it.

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.