MacBook Forgets All Settings

The last couple of days something strange has started occurring on my MacBook. Whenever I reboot, my Mac seems to forget a lot of settings. It forgets what AirPort network I was connected to, my sound volume, the order of my menu bar icons, what icons I have turned off, my display profile, my appearance settings, and probably a whole bunch of other things which I have yet to notice. After the settings are forgotten, I have to manually go change each setting back to its original setting except for one, the color profile. I can't figure it out, but when I bring up the color profile setting, without clicking anything my MacBook instantly remembers.
So what's going on and how do I fix this? I can't really pinpoint what happened when this issue started up. The only thing I notice is my bootup times are now a lot longer. That's about the only thing different. So any ideas on what's going on? By the way, I have tried reseting my PRAM.

I have tried reseting NVRAM. On an Intel machine, reseting PRAM and NVRAM are the same shortcut. I also tried reinstalling the 10.4.7 Combo update. The first time it booted up after installation, my settings were intact. However, each reboot after continued the trend of loosing settings. I have also repaired my disk permissions.
Now playing with the user accounts has been very odd. The second user account so far has not had an issue, but it has shown me something weird with my current user. If I log out and log back in, my settings are correct, even if they weren't when I booted up. If I don't set my user account to auto login, my settings are retained after a reboot when I first log in. I just find this behavior very weird.
Another thing which I have noticed is I'm now loosing certain settings after a sleep. I loose my Airport connection, my sounds, and my appearance settings when I wake from sleep. It's not every time, but maybe 50% of the time.
Any ideas on what my next step should be? Also, does anyone know where these settings are stored? Are they stored in PRAM or the hard drive? Is their a preference file I can just delete and have it recreated on a reboot? Thanks in advance for any answers.

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