OS X 10.5.4 ignoring my preferences settings

I posted this question under a different heading, but after thinking about it I think the multiple symptoms are all attributable to OS X ignoring my preferences settings. I'm experiencing the following problems.
First, after working fine for months (since I got the computer), my mouse no longer registers my right clicks. The right mouse button works just like the main mouse button, even though my preference settings are for the right mouse button to be enabled.
Second, after working fine since the beginning, Spaces no longer opens applications in the space they are assigned. E.g., I have safari and mail assigned to space 2, and word and excel to space 1. They used to open correctly in their assigned space, but now they all open in whichever space is the active one. Again, the settings in the Spaces pref's pane remain unchanged.
Third, I had set my security preferences to require a password to wake from screensaver. The preferences remain unchanged, but now the computer wakes from the screensaver without requiring a password.
Fourth, I have the program "Text Expander" installed. It works as a preferences pane, but now no longer functions even though all settings in the preferences pane for the program remain unchanged.
All of this started last week. Logging out and back in does not correct the problem. I tried rebooting on Friday, which did solve all of these problems. After coming back to work after the weekend, the problems are back, and rebooting no longer solves them. I also tried trashing my finder preferences, but this did not seem to help.
Any advice appreciated.
- Tom

Thank you for the reply and the advice. I downloaded MainMenu and ran the various scripts, including repair permissions, and then rebooted. This didn't fix the problem. I then added a new account to see if the problem was restricted to my own account or was system wide. The new account worked properly, and then after switching back, my main account also worked...
Until this morning, when it was not working again. I rebooted again, and currently the Mac is responding to the System Preferences settings. (We'll see how long this lasts, though.)
A couple of additional things I noticed while the Mac was not responding to system preferences:
Fast user switching, although enabled, did not work and the account name did not appear in the menu bar;
Items that I had dragged off of the dock reappear after logging on again.
Thanks,
Tom

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