10.5.8 Software update screws permissions

I had a recent disk crash on my MacBook, so bought a new hard-disk for it. I installed OSX with the original disks that I have. That is to say I did the following:
Install 10.4 with 2 disks
Upgrade to 10.5 with the official upgrade disk
All seems to work fine at this stage. So I installed some additional software and everything works fine. Then I did the Apple Software Update (from the menu in the top left corner). Amongst other things, this installs Safari 4.0.3 and upgrades the OS version to 10.5.8.
Next time I boot up, I find out that Firefox doesn't load up. Some searching around the net and I find out that this might be related to disk permission problems. It's at this time that I discover that I am unable to create any new folders on my Desktop. The error reported when I try to is:
The operation could not be completed
An unexpected error occurred (error code -8058)
I run Disk Utility, and find a few hundred disk permission problems. "Repair Disk Permissions" button reports that it fixes all issues, but running the check again finds just as many violations.
To make sure that it wasn't something i did, I formatted the disk again, and re-installed the OS. But applying the updates screws up my permissions again.
So: the underlying problem appears to be with permissions. This manifests itself in several ways, including this problem with my desktop. To repeat, I cannot interact with the desktop itself (the computer background), although I can access it via the Finder. (e.g. Any USB files I add to the system don't appear on the desktop, but do appear in the desktop directory in the Finder).
Other problems that I've found (I suspect this is not an exhaustive list):
- Cannot redeploy DMG files (I tried to download and redeploy MacOSXUpdCombo10.5.8.dmg after finding suggestions that this might fix my problems). I then found that other DMG files don't work!
- Some programs (most notably Firefox) simply won't open (even in safe-mode).
Does anybody have any ideas as to what might be going wrong? And how I can fix it?
It can't be a compatibility problem with the specific hard-disk that I replaced - can it?
Thanks,

Thanks Kappy.
I followed this technique on my third re-installation with no success. I did it a fourth time, and instead of running the unified 10.5.8 update, I ran each of the 10.5.x updates individually. (10..5.1 followed by 10.5.2 etc.) This frustrating and time-consuming work-around seemed not to replicate the problem again, and I've been running happily for 2 weeks since.
However, after attempting to install a third party application tonight (a free app from the Web that I hoped would help me re-import my lost iTunes library from my iPod, an application I hasten to add, which I need because iTunes itself won't let me recover my library from my iPod), the whole system hung again, crashing the Finder app. After an leaving the system alone for an afternoon in order to allow Finder to recover itself, I forced a reboot. Now I find that I am unable to write anything to my desktop again. The original problem is back!!
I'm very frustrated at the moment as I am unable to pin down the cause exactly. Certainly however, there is something very unstable about the MacBook's setup! I'm pretty sure it's down to one of the following:
1) The OS has some kind of allergy to the particular brand of hard-disk that I've put into my MacBook after the original crash. This I find fairly unlikely, although I'd like to hear someone else's opinions and experiences on similar matters.
2) 10.5.8 has a bug in it. My chief suspects are the reported disk permission issues, much discussed in these forums. I strongly suspect that they are not quite as innocent as Apple make them out to be: http://support.apple.com/kb/TS1448
I'm going to reinstall my OS for the 5th time now. I will only upgrade the OS to 10.5.7 and run with that for a while to see what happens. If I run happily for a month with this setup, I would very much like to report this as a 10.5.8 'issue' to Apple. Does anyone know how I can do this in an official capacity?

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