Dock won't hide/show after Tiger security update

I installed the Dec 27 Tiger security update last night (via SW update) and now the dock is behaving badly. I had it set to automatically show/hide, but it would not show anymore after the update. I always install sec updates, so I did also do the previous one without any problems.
So far I've done this to try to solve the problem:
- I changed the settings to turn hiding off and the doc appears and works correctly in that mode. The only problem with it seems to be that it won't show after it hides with hiding turned on.
- I repaired permissions
- I shut down and restarted
- I did a safe-mode restart and a regular restart
- I trashed my doc preferences, restarted, and recreated the configuration of items I like.
- I tried removing the preference called /Library/Preferences/com.apple.dockfixup.plist which had no effect, so I put it back. (It's dated 2006 but I have no further info about it.)
Also, oddly, it seems that my system menus are strictly pull-down now. I am almost sure they had some drop-down behavior before, because I keep clicking on main menu items expecting the submenu to persist, and it doesn't. If I'm not imagining this, perhaps the two issues are related?
I don't have any system mods or Finder replacement apps.
Are there any other dock-related files that I could replace from my backup to try to fix this issue?
Did the update do something specifically to change the dock?
I really hate to reinstall and reupdate from scratch to fix such a minor problem, but it is 100% annoying. Ideas and commiseration welcome.

Thank you. I didn't know you could remove the whole folder without wreaking havoc. I will try another user account for thoroughness.
New info:
I discovered this morning that both of these problems do not occur with my Contour mouse, only with the Logitech trackball. The trackball has a brand new problem at startup today, which is that it acts like it's constantly right-button-down. It selects only.
So perhaps its a driver or mouse hardware issue. I think it's suspicious that it started immediately after the update, but since the trackball did not come with a driver, I am not sure I can further troubleshoot it myself. I'll dig around in the system and on the net a bit to see, but I'm probably going to buy another pointing device in order to resolve this. The trackball is only about 2 months old, but maybe it's filled up with cat hair. ... There's a joke in there somewhere.

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    Owners Enabled : Yes
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    Can Repair Permissions : Yes
    Can Be Verified : Yes
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    Bootable : Yes
    Supports Journaling : Yes
    Journaled : Yes
    S.M.A.R.T. Status : Verified
    Disk Number : 0
    Partition Number : 3
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    Hi Magsrobby,
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    BTCare Community Mod
    If we have asked you to email us with your details, please make sure you are logged in to the forum, otherwise you will not be able to see our ‘Contact Us’ link within our profiles.
    We are sorry but we are unable to deal with service/account queries via the private message(PM) function so please don't PM your account info, we need to deal with this via our email account :-)

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