I'm guessing the Supra software was designed for 1.3; try prepping the hard drive with HDToolBox if you can. I recommend using the HDToolBox version from the 3.1 Install disk, since it has a few improvements. It works under Kickstart 2.x. Use the Tooltypes to change it to scan for Supra's device driver (which is probably something other than scsi.device).
It sounds like the Supra software messed something up with the RDB, so you'll probably want to recreate it from scratch. Once you're in HDToolBox, change the drive type, define new, and read the drive parameters.
Also, you shouldn't need to low-level format drives anymore - that's a vestige of 80s hard drive manufacturing techniques.