I've experienced this too, especially since I run as a non-admin user for safety reasons. It's also a good reference on enabling and disabling "root". Nowadays it's best to keep "root" disabled.
A relatively trivial annoyance for several years, I've hated the fact my preference to change the Finder's windows to column view never seemed to 'stick.' I finally discovered that this apparent bug is actually a feature: The only folders your preferences will 'stick' on are the folders in your own home folder. Since permissions are an issue, nothing outside of it will adhere to your preference.
Enter root. Open Applications: Utilities: Netinfo Manager, then choose Security: Authenticate, enter your admin user password, then choose Security: Enable Root User, and provide the root user its own password. Now switch over to System Preferences: Accounts, and select the Login Options button at the bottom of the account list. Make sure that the the 'Display Login Window as' option is set to 'Name and password.'
Log off and back on as username 'root' (with the new root password). Once logged in, open Finder: Preferences: General, and check the 'Open new window in column view' item. Log off root, login as your normal user again, and now, every user will benefit from the much more productive column view as the default ... finally!
[robg adds: I would also recommend opening NetInfo Manager again and using Security: Disable Root User (after authenticating again) to disable root.]
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