Does your SCSI card reader use one bus ID and then every card in the reader then have its own LUN? Never used one of these card readers before, but they sound good.
Just a silly theory, but is it something such as the Amiga only wanting to boot from the first LUN? What cards can you see from the early startup menu?
Because you're cold booting from OS3.1 ROM then it'll be using the older scsi.device or whatever the A2091 uses. Does it make any difference once the machine is running from the OS3.9 ROM? i.e. enter early startup menu with 3.9 and see if any of the other card LUNs are available.