First of all, your BOOT Hard Drive should ALWAYS be set to ID # 0. Your next SCSI device should be set for ID # 1 and so on. The higher the ID number the lower the priority. For some strange reason the A2091 SCSI Controller card loves Quantum Hard Drives the best. Did you use the A2091 Installation software disk? If you did not, you really should. Here are the instructions for properly installing a new hard drive on an Amiga 2000HD. I am assuming that you are booting from the A2091 Installation Software disk, like you should be doing. Before you begin, make sure that the A2091 disk is NOT write protected (the new hard drive parameters MUST be written to the A2091 Installation disk. Ok, here we go....
First, boot up your Amiga 2000HD with a copy of the original Amiga A2091 Installation Software disk. Make sure that disk is write enabled. Then load up the HDToolbox. The first thing you have to do is to define the new drive type and save it to the disk in DF0. If you do not do this, the Amiga 2000HD will not know what type of a hard drive is installed. To do this: Click on Change Drive Type on the Hard Disk Preparation, Partitioning and Formatting screen. Then click on Define New Drive Type. You can type in the drive's specifications, or you can have the system try to read the drive's specifications by clicking on Read Configuration from Drive. When the correct specifications are selected, then click on OK to return to the Change Drive Type screen. Then click OK again. Next: You MUST Low-Level Format the Hard Drive. After formatting is complete, click on Verify Data on Drive. This will check the hard disk for bad blocks. Next Partition the hard drive and save the changes to disk. Now, reboot your Amiga (warm reboot, NOT COLD). Finally, click on each hard disk partition icon and select Initialize from the Workbench menu. What revision are the BOOT ROMs on your A2091 card?
Revision 4.0 = 512 Megs or lower Hard Drives
Revision 6.6 = 1 Gig or lower Hard Drives
Revision 7.0 = up to 4 Gigs, but NOT higher!
I hope that I have helped you :-D