Problem with permissions after NOT installing 10.5.3

A few weeks ago when Software Update asked me if I wanted to install 10.5.3 I said no, since I wanted to wait for a while to see if there were any problems first before I went ahead with it. According to Software Update, 10.5.3 has been downloaded on my computer, but not installed, although I can't find it anywhere.
Ever since then things have been getting increasingly weird. I thought I had most of the problems solved after booting from the Leopard disk and repairing ACLs and permissions. However, after I shut my computer down for the night, and rebooted the next morning, all my problems were back and a few new ones. Now I have to log in each time I reboot the computer. I have to log in each time I open Mail. I can't unlock anything. I click the lock and nothing happens. Time Machine has stopped working again and is no longer backing up my data. When I click on "Get Info" for my HDs or apps, Sharing and Permissions says I have custom access - all the rest is greyed out, and I can't unlock anything. I seem to have lost permission to make any changes! Very frustrating!
Any suggestions would be appreciated.

Yes, I can access the Time Machine application.
Following up on your previous suggestion, even though I'm listed as admin in the Accounts pane, I thought it was worth a shot, so I followed the steps set out in the Apple article TS1278: "Mac OS X 10.5: Administrator user changes to standard".
After booting from my Install DVD, and resetting the password for the System Administrator (root), I restarted from my Mac, selected "Other" in the login window, and tried to log in as System Administrator (root) with the password I'd chosen, but it wouldn't log me in. All that happened was the login window trembled a bit, then cleared, and that was that. I tried a number of times, with the same result. Do you have any idea what I can do to correct that? Because it sounded like the process described in this article could very well fix my permissions problems.
Thanks for your help.

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