However...for some strange reason I cant see any of my HDs in HD Toolbox despite the fact that I am actually booting on one of them.
That's not right. Make sure the device (or scsi_device as it is on my 3.9 system) tooltype for HDToolBox is set to scsi.device.
Someone else already mentioned this but do make sure that one of your HDs is a master and the other is a slave. I kinda doubt this is the problem as your system probably wouldn't boot if they were both masters, but ya never know.
Of course it could also be a cable problem. Btw, does the drive powerup? Do you hear it spin up when you turn on the Amiga?
- Mike
