I updated the Apple Discussion forum with my results and I'll share here.
The problem:
After applying the 10.5.8 Combo update, the permission database is not updated. If you VERIFY permissions after installing the Combo update, you'll notice a bunch entries looking for permissions to be set to ?---------. If you REPAIR permissions, it will actually set all those files to ---------.
I have no idea of what may happen because of this, or whether it needs to be fixed or not.
There are a couple fixes out there, but I took the safest path. I fixed this issue on both my Macs by simply REINSTALLING the 10.5.8 Combo update again TWICE.
Here's what I did:
The Fix:
1) Installed the Combo 10.5.8 update again (this is the 2nd time installing the update)
2) VERIFIED permissions - still incorrect (OPTIONAL)
3) Installed the Combo 10.5.8 update again (this is the 3rd time installing the update)
4) VERIFIED permissions - this time permissions correct no ?--------- entires.
5) REPAIRED permissions - everything still correct
If you are looking to solve this, you don't have to VERIFY permissions after installing the update the first time, I was just doing it to see if they were still messed up.
So the key seems to be to apply the combo update twice in a row for the permissions database to be correct. You cannot REPAIR permission in between either.
I did this on both my Macs and both are fine, they don't report the ?--------- permissions anymore.
Because I REPAIRED permissions after that first initial 10.5.8 Combo update, I needed to install the Combo update TWICE more (for a total of 3 times). I'm guessing that if you just installed the Combo update, but haven't REPAIRED permissions yet, you can solve this by just re-installing the 10.5.8 Combo update again (for a total of 2 times). You can VERIFY permissions to check, since VERIFYING permissions don't not change the files.
As for anyone curious about the Time Machine backup after reinstalling the Combo update again, it does require the DeepNodeTraversal again, however, it only copies about 350MB of files, as opposed to the 2+GB after the first Combo install.
-Kevin