Repair Permissions differences between Onyx and Disk Utility

If I repair permissions, there are a large number of 'repaired permissions' if I switch between using Onyx (10.6) and Disk Utility. Most of them are in
System / Library / CoreServices
System / Library / Java
System / Library / Frameworks
Why should this be? It makes me think that either Onyx or Disk Utility is doing it wrong. If I had to back which one it is, I'd have to say Onyx is the likeliest suspect. In other words should I avoid using Onyx to repair permissions and just use DU in future?

should I avoid using Onyx to repair permissions and just use DU in future?
Probably, but some permission results are always and repetitively wrong:
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.

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