Missing desktop items... privileges wonky

I have a weird problem. I have just had to reformat and reinstall everything on my computer. I have successfully completed about 90% of the job. All of the sudden I can't see what should be on my desktop and I can no longer install software to the Applications folder. I have Admin privileges so I thought I had a permission problem. I rebooted from the install CD and repaired the disk permissions. I rebooted when this process was complete and checked the permissions set for my desktop and the Application folder. All seems to be as it should be. When I log in, I seem to be getting to my desktop and everything seems to load fine (Although I still can't see drives and other items on my desktop). Suddenly, I get a blue screen for a second or two and then I get a blank desktop. I can see my dock, I can access my drives by pressing shift-command-c, but I have nothing on my desktop (I should have) and I also can't install software to the Application folder. Any ideas what is going on and why I can't install software or see m desktop items?
Power Mac G4 (AGP graphics) Mac OS X (10.4.3)

I had a similar problem when I updated to 10.4.3. If
you have Stuffit make sure it is version 10.0 or
greater as lower versions interact with OS 10.4.3,
and prevent it from finishing loading Spotlight and
other things.
Thanks for the idea. I tried loading the latest version of stuffit and redoing the permissions.... Still have the same problem. Although, now I can install software. I simply cannot see my desktop items. I get to a desktop alright but there are no items showing on it (drives of any kind, a bunch of files I know are there, etc...). I can access MY desktop by using the shift-command-c key strokes and navigating to it, but I can't see the items on my desktop proper.

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