Getting HD's to work in Amiga's sometimes is one of the more frustrating aspects to the damn things.
Are you 100% positive that the tooltype in HDToolBox is set to the proper SCSI card? Did you try un-terminating it? Don't laugh too loud... that's brought back drives from the dead for me. lol
Also, what ROMS are you using in that A2091? Want to make sure they're 7's and maybe check the other jumper settings (there's 3 that are relevant to SCSI stuff I believe) while you're at it. Or are you saying the card AND drive work in your A3000?