I recently came up against a problem after backing up a client's PC to an external HDD. I use this storage for my Ubuntu (Intrepid Ibex) system, and after doing some file maintenance, I saw that there was a folder that couldn't be deleted, even by root.
Permissions were set correctly but that wouldn't have mattered anyway since I was logged in as root. I couldn't remove the file by using the INODE trick so I ventured back into the world of Windows XP.
After some rooting around hehe I managed to find a forum post detailing a very quick 2 line cmd file that reset the permissions on the file/folder from a Windows perspective. This led me on to an improved version of similar software that had been written by a guy named Chieh Cheng, released under the GPL:
His scripts enable you to simply drag and drop a file/folder on to the script and then gain control by changing/resetting the permissions. His scripts were an absolute godsend and enabled me to reset and delete the folder in question. I have a feeling that the folder in question may have been created by a trojan/virus on the client's PC.
Hope this helps if you get stuck in the same situation.