Given that jumpers are set correctly, cables are connected properly, the power supply is strong enough and HDToolbox is configured correctly, then if HDtoolbox does not show the drive, no other software will show it, too.
If the drives are IDE they might suffer from the "slow spin up" problem and might be seen after a reboot. They might also show up if you run a software like IDEfix which reinitializes the IDE bus.
For SCSI, if you have a SCSI controller from Phase5 you can use the UnitControl program to rescan the bus for drives which were not recognised on power-on.
