The Mac OS X 10.5.8 Intel Combo update installer is buggy and is causing an unusual problem. My suggestion is to wait until the problem have been sorted out.
If you want the rundown on what's going on, check out MacFixIt.com, who are keeping track of it all.
Personally, this is the first time I have had any major trouble with an Apple update. I got hit by the damaged permissions bug in the installer. That fact that I was updating Mac OS X 10.5.8 Server did not make the problem any more pretty. The first symptom I had was being unable to run certain applications. Example: MacTracker throws up a warning box that my administrator account does not having sufficient permissions for a variety of directories. I don't suggest trying to fix these permissions problems as apparently they go into the ACL level, and unless you are an expert, (I'm not), I'd move along to one of the currently suggested fixes:
The current best suggestion for performing the installation of Intel 10.5.8 via the Combo update installer is below. Please don't fall over when you read it. I know. No normal user will tolerate this:
1) Repair the volume.
2) Repair the volume's permissions. Ignore the never-fixed permissions you see over and over and over. That was a bug from the 10.5.7 installer. (o_0)
3) Download the Combo installer from Apple's site.
4) Boot the volume into Safe Mode.
5) Install using the Combo 10.5.8 installer.
6) Let the Mac go through its 2x restarts.
7) Do NOT NOT NOT then repair permissions.
8) Reboot into Safe Mode again.
9) REINSTALL the Combo 10.5.8 installer AGAIN. (Yes, again.)
10) Let the Mac go through the 2x restarts, again.
11) NOW repair your permissions.
At that point you 'should' be OK. But don't take my word for it.
Simply put: Part of the installation process involves permission changes involving a database on the Mac. Part of the script for the installation is wrong and does not finish the process correctly. You have to perform the installation a second time for the script to use the permissions database correctly. If you only install once, then repair your permissions, you're actually damaging the permissions, giving them wrong settings. The second installation will solve the problem, as long as you have NOT repaired your permissions yet.
Happy me lives on the bleeding edge and did not know about this mess. I followed the usual rules, which messed over my server update. I then compounded the problem by trying to compensate for it by DIY permissions repair. Despite the fact that I set everything so it 'looks' good in the GUI, down deep in the ACL settings I made scrambled eggs. I am now going to have to reinstall the OS from scratch. Thankfully I am used to such stuff. But your Aunt Mabel is going to scream bloody murder if she has to perform this dancing act. Hopefully Apple will update the installer script ASAP.