I also had this problem when I use my 2 GB harddisk.
When you installing OS 3.9 you get a question about 4-way IDE adapter. Select this. After the installation you change the Maxfiletransfer in HDtoolbox to fffe0.
My problem also disappear when I use a Hitachi/IBM or Toshiba notebook HD. I only had problems with a Fujitsu HD.