You have raised a good question. Unfortunately, the most definitive descriptions I have seen of the automatic defragmentation predate ACLs, and until the release of the Mac OS X 10.5.8 Combo Updater, I had not seen so many references to files with permissions beginning with 000.
I applied the Combo Updater, and then repaired permissions and looked for files with permissions beginning with 000. I found quite a few by using this Terminal command:
sudo find -x / -perm 000
The easiest solution is to reapply the Combo Updater, and leave the permissions alone.
There is a lengthy discussion of the
000 permissions problem (to give it a name) in the Apple Discussions Forums.
