I have a client with the same problem. They are using Windows XP and W98 workstations running from a Linux server. Nothing has changed there since the original install (that I know of), but I am unable to install any upgrades or PTFs. I am able to manually create, modify, or delete files in all of the necessary directories, so I know that I have full rights.
I am also anxious to find the answer to this problem
-Phil