Dock and sidebar preferences won't reset

Greetings all,
Several applications appear as question marks in my Dock. When I drag them out, they reappear when I restart or log out and in again. In fact, my Sidebar reverts to a past version as well under the same conditions, so I wonder if these problems are linked. Additionally, applications' Recent Items do not update properly, returning to a fixed state from long ago.
I've trashed my homedirectory/Library/Preferences/com.apple.dock.plist and dock.db files, tried killall Dock and tried restarting, but no new .plist or .db files are created. I've gone in to the Property List Editor and deleted the persistent apps that cause the problem, but PropertyListEditor says I cannot save the document. I've created a new user and copied their .plist and .db files but they once again cannot be modified, either by direct editing or by dragging items into or out of the Dock or Sidebar. Nothing has worked.
I fear I may have to wipe my computer clean and do a fresh install of everything to get rid of these problems, but I'm hopeful that someone can identify what's wrong so I can avoid that! I'd be grateful for any suggestions!

+ at the end means that ACLs are present. there are some default 'deny delete ACL's on many system created folders including your library folder etc. that's the main reason not to use 'apply to enclosed items" on such folders. I don't know why they are missing on your main account that that should not hurt anything. still I suggest you reset permissions adn ACLs on your main home directory as follows.
first run the following terminal command from your main account
sudo chown -R `id -un`:`id -gn` ~
Then follow the instructions in this KB article
http://support.apple.com/kb/TS1334?viewlocale=en_US
use your SL disk instead of the leopard disk as this article mentions. see if any of this helps.

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