Weird Locked Files/Permissions/Dock/Etc

Question

I have some sort of odd locked file/permissions problem (I think).
About a year ago, I seem to have done something to my permissions or locked files that I can't seem to fix.  I have a variety of disparate symptoms, including applications that won't work or can't be installed/deleted because support or preference files are locked or can't be changed, a need to repeatedly reauthenticate with a password just to move files from one folder to the next, an inability to turn off file sync for mobile me, dock item changes that go away whenever I reboot, locked files that continually reopen in Preview, having to manually delete and reinstall apps like Preview apparently because of locked preference files, printers that won't work because of locked files until I delete all and reinstall, software that won't run properly or fails to launch at all on double click, etc.
It is almost like a ghost in the machine problem because the problems are relatively varied.
I've tried disk utility etc to repair permissions and none of the repairs work (I keep getting the same errors, copied below).  I've tried a complete reinstall of the OS, repair permissions from the OS X restore disk, etc. and nothing seems to help.
This is happening on a Mac Pro 1,1 (3.0 GHz), running 10.7.4 with all updates through today and with a Radeon 4870 card, and 9 GB of properly matched ram.  Everything else works pretty well and I have no similar problems on my wife's 2011 iMac, my MacBookAir i5, etc.
I'm thinking that there is some sort of locked file or permissions problem that is not getting fixed correctly and that there might be some trick to fixing it.
Help!!
Repairing permissions for “Master”
ACL found but not expected on “Library/Printers”
Repaired “Library/Printers”
ACL found but not expected on “private/etc/apache2/users”
Repaired “private/etc/apache2/users”
ACL found but not expected on “Library/Printers/PPDs”
Repaired “Library/Printers/PPDs”
ACL found but not expected on “Library/Printers/PPDs/Contents”
Repaired “Library/Printers/PPDs/Contents”
ACL found but not expected on “Library/Printers/PPDs/Contents/Resources”
Repaired “Library/Printers/PPDs/Contents/Resources”
ACL differs on “Users”
Repaired “Users”
ACL found but not expected on “private/var/root”
Repaired “private/var/root”
ACL found but not expected on “private/var/root/Library”
Repaired “private/var/root/Library”
ACL found but not expected on “private/var/root/Library/Preferences”
Repaired “private/var/root/Library/Preferences”
Permissions repair complete

Answer 1

Repairing the permissions of a home folder in Lion is a complicated procedure. I don’t know of a simpler one that always works.
Back up all data now. Before proceeding, you must be sure you can restore your system to its present state
Launch the Terminal application in any of the following ways:
☞ Enter the first few letters of its name into a Spotlight search. Select it in the results (it should be at the top.)
☞ In the Finder, select Go ▹ Utilities from the menu bar, or press the key combination shift-command-U. The application is in the folder that opens.
☞ Open LaunchPad. Click Utilities, then Terminal in the page that opens.
Drag or copy — do not type — the following line into the Terminal window, then press return:
chmod -R -N ~
The command will take a noticeable amount of time to run. When a new line ending in a dollar sign ($) appears below what you entered, it’s done. You may see a few error messages about an “invalid argument” while the command is running. You can ignore those. If you get an error message with the words “Permission denied,” enter this:
sudo !!
You'll be prompted for your login password, which won't be displayed when you type it. You may get a one-time warning not to screw up.
Next, boot into Recovery by holding down the key combination command-R at startup. Release the keys when you see a gray screen with a spinning dial.
When the Recovery screen appears, select Utilities ▹ Terminal from the menu bar.
In the Terminal window, enter “resetpassword” (without the quotes) and press return. A Reset Password window opens. You’re not going to reset the password.
Select your boot volume if not already selected.
Select your username from the menu labeled Select the user account if not already selected.
Under Reset Home Directory Permissions and ACLs, click the Reset button.
Select  ▹ Restart from the menu bar.