10.5.4 update messed up my dock.

I installed the 10.5.4 update and my dock now doesnt have a border around it or the little glowing dots that let you know an app is open. It also crashes when i try to drag something off the dock. My stacks dont have a background either, its just icons. What can i do to fix this? I tried running Onyx to clean out all the caches, but that just made my finder, dash, and trash icons disappear.
Here's a pic:
http://i9.photobucket.com/albums/a93/canada2113/Picture1-9.jpg
Message was edited by: NoSmokingBandit

Did everything you said, not a big help. I did notice, however, that with my dock on the bottom my windows are reflected as well as the icons. Kinda cool-looking, but not good i suppose.
Perhaps i should re-install the update .pkg with pacifist and see if that gets it all in line?
Heres a pic of the reflecting windows in the new admin acct i created (they reflect in both accounts, i just happen to have the new one open at the time):
http://i9.photobucket.com/albums/a93/canada2113/reflect.jpg
Thanks for the help so far.

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    [2012-09-07 20:40] upgraded pkg-config (0.27-1 -> 0.27.1-1)
    [2012-09-07 20:40] upgraded sane (1.0.22-9 -> 1.0.23-1)
    [2012-09-07 20:40] upgraded sdl (1.2.15-1 -> 1.2.15-2)
    [2012-09-07 20:40] installed lib32-v4l-utils (0.8.8-1)
    [2012-09-07 20:40] upgraded skype (4.0.0.8-1 -> 4.0.0.8-3)
    [2012-09-07 20:40] upgraded sudo (1.8.5.p3-1 -> 1.8.6-1)
    [2012-09-07 20:40] upgraded vim-runtime (7.3.600-1 -> 7.3.659-1)
    [2012-09-07 20:40] upgraded vim (7.3.600-1 -> 7.3.659-1)
    [2012-09-07 20:40] upgraded vlc (2.0.3-2 -> 2.0.3-3)
    [2012-09-07 20:40] upgraded wireless_tools (29-6 -> 29-7)
    [2012-09-07 20:40] upgraded xorg-server-common (1.12.3.901-1 -> 1.12.4-1)
    [2012-09-07 20:40] upgraded xorg-server (1.12.3.901-1 -> 1.12.4-1)
    [2012-09-08 12:19] Running 'pacman -S libreoffice'
    [2012-09-08 15:48] Running 'pacman -Syu'
    [2012-09-08 15:48] synchronizing package lists
    [2012-09-08 15:48] starting full system upgrade
    [2012-09-08 15:48] warning: /etc/pacman.d/mirrorlist installed as /etc/pacman.d/mirrorlist.pacnew
    [2012-09-08 15:48] upgraded pacman-mirrorlist (20120626-1 -> 20120908-1)
    [2012-09-08 15:48] upgraded ppp (2.4.5-3 -> 2.4.5-4)
    Last edited by sim590 (2012-09-11 19:20:46)

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