I am not responsible for the Eraser manual, but I did write a piece in the FAQ (link below) on Getting to know Eraser 6. There are instructions there both for erasing the free space on a drive from the context menu and for creating a task in the Schedule. If there is any way in which you think these instructions can be made clearer, please let me know; I am always willing to update the post as necessary.
In Vista and Windows 7, there is a whole range of files (tens of thousands of them) that are heavily protected by the OS, and to which users (even running as administrator) will never have any form of write access. These files simply cannot have their cluster tips erased. With an OS that is installed to a new or clean hard drive, that will typically not be a major problem, as most of these files are written to the drive on first install, and their cluster tips will not contain private data (or any real data at all), though obviously this becomes less true as the OS is progressively updated and files are replaced.
So your 'error' message is not really an error at all. I am encouraging Joel to downgrade or remove error messages relating to issues that are built into the OS; he has already done this to some extent in the Eraser 6.1 development builds, and there is a Trac ticket to reduce (or even eliminate) the log entries related to system protected files.
Incidentally, I believe that, for the great majority of users, cluster tips represent much less of a security/privacy issue than, for example, application logs, shadow copies and the page file. You need means other than Eraser to deal with all of these. Computer security is not a one stop shop.
David