The HDToolBox isn't reading the drive geometry correctly. You probably need to get the specs (heads, cylinders, etc.) from the manufacturer and enter them yourself.
I have a 20GB IBM/Hitachi in my A1200 that was detected correctly. But, in my A4000D the WD 120GB came up as 35GB. I had to manually enter all of the geometry (as well as do some LBA math).
As stated before, without additional software, you should keep the partitions below the 4GB boundry. (Otherwise, anything written above 4GB will overwrite the start of the disk.)
