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:
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:
d = directory
r = read
w = write
x = executeable program
| | |
| | all other users not in first two types
a little more info
Before the user had read & write. A member of the group had read.
After, only the user had read & write.
If you are running Panther or Tiger: