When you put the jumper on do you have a SCSI disk on board ? Or an external SCSI disk ?
If not then I guess it's trying to find the boot block on an attached SCSI disk.
I never used it for disk myself, just used it for the scanner using the gvpscsi.device (I think .. use a sysinfo app that lists out the devices to be sure)
I also seem to remember there being a specific Hard Disk formating/configuration tool for it.
Sorry this is all coming from memory, not had an Amiga for a while now.
Good luck!