Under 2.2.2 Manual Installation there's a link to
http://www.tacp.toshiba.com/tacpassets-images/firmware/MESV12US.zip which I downloaded.
Under "Dual Boot" it states that I should extract the file nk.bin from the above zip file.
The problem is that the zip file contains just an ISO file, which, when burnt to CD contains an .exe file and an autostart file. The .exe file reflashes the Gigabeat, but there's no sign of any nk.bin anywhere, so I can't set up a dual boot as per the instructions.
Secondly, I decided to try the single boot instead, so ran beastpatcher as per the manual, which flashed the Gigabeat. However, all that results in is that I can see the small boot partition of the Gigabeat's hard drive, but lose access to the main partition.
Reflashing with the Toshiba software restored my Gigabeat.