I would check the scsi device name--it must correspond to the scsi board used. On the A4000D, HDToolbox is set up for IDE. Open the tools folder, select HDToolbox and click information on the icon menu(or left A key i). There will be a line in the tool types box that reads:
"SCSI_DEVICE_NAME=scsi.device" for the built in IDE of the A4000D. If you want to use the GVP card, you have change this to "gvpscsi.device". Other cards from other manufacturs will have different device names. If you don't have the autoboot enabled on the Gvp card, you have to have a file called "gvpscsi" in your expansion drawer. This is on the install disk which also contains gvp's own hard disk partitioning software.
Once you have the correct scsi device name in the tool types of HDToolbox, it should recognize the drive and you should be able to partition it and have the partitions recognized.