Lion: Dock settings revert after logging out or restarting
Yes this sounds like a permissions problem - probably the permissions on the Dock's settings files are wrong.

The easiest way to fix it is to delete these files. You'll find the config file at 

~/Library/Preferences/com.apple.dock.plist

Make a change to the dock and it will then regenerate them with the correct permissions. Do note that you shouldn't lose your Dock settings this way, but it is a possibility. In any case, the Dock is easy to configure back the way you want it.

If that doesn't work, try deleting:

~/Library/Preferences/com.apple.dock.db

as well.

Hint: A clue that the permissions on them are wrong is if OS X prompts for a password when you try to delete these files - it shouldn't.