Dock problems bright dot showing open apps missing and other strangeness

Question

This is on a an early MacPro: see end of msg for spec.
After installing the 10.6.2 upgrade my dock as been behaving oddly: the bright spot showing that an application in the dock is active is only seen under the finder application. and right clicking on the icon of a running application shows only 'open' and 'options' as choices (no quit).
Right clicking on the Finder application shows "Application not responding" and restarting the finder in force quit has no effect (note the finder is not shown as non responsive in the force quit app)
launching an application that is not in the dock does not cause its icon to show up in the dock.
I attempted to rerun the 10.6.2 updater but of course it reports that it is already installed
Otherwise the computer seems to be running normally and yesterday I did the LED Cinema Firmware update with out a problem (I am so dumb I did not even know it had an iSight camera and was still using my old Firewire iSight)
What do I try next
Hardware Overview:
Model Name: Mac Pro
Model Identifier: MacPro1,1
Processor Name: Dual-Core Intel Xeon
Processor Speed: 3 GHz
Number Of Processors: 2
Total Number Of Cores: 4
L2 Cache (per processor): 4 MB
Memory: 6 GB
Bus Speed: 1.33 GHz
Boot ROM Version: MP11.005C.B08
SMC Version (system): 1.7f10

Answer 1

Windshadow99 wrote:
Some strangeness I went to look for those 2 files just in case and found that the homedirectory/library was locked and OS said I only had read on that folder Yet all users except guest user are admin and should have full Privileges. I looked at the main Library on the boot disk and did not find the files you mentioned the closest was diskname/library/com.apple.dockfixup.plist and com.apple.loginwindow.plist and com.apple.loginwindow.plist-orig
of these only com.apple.loginwindow.plist shows that it was modified at the time I changed user and back.
DO NOT touch those files. you are looking in the wrong library. every user has its own home directory in /Users. you can get to it by clicking on the house icon in the sidebar or by going to Hard drive->Users. by default only the current user has write access to its home directory. as an admin user you can give yourself right to other users home directories but there is normally no need to do this and it's not the default.
the dock preference file in the other user has nothing to do with the dock preference file in your main user. I don't know why rebooting didn't help but logging in as another user did. I asked you to log in as another user because it would have a clean dock preference file so if the problem was with the preference file corruption for the main user it will be immediately clear.
so, log in as the main user, click on the house icon in the sidebar of any finder window and go to Library->preferences. com.apple.dock.plist is there. you can delete it or move it to the desktop and log out/in. that will recreate that preference file from scratch with default settings and clear any corruption it may have had.