First off, you don't have to look in the startup-sequence, I think the poster means the "Expansion board diagnostic..." in the "Early startup control" menu. Startup-Sequence is a text file with commands executed when booting, and that obviously needs to harddrive to be present in order for one to look in it.
Which GVP controller is it? If it's a GP HD8+ like mine, have you set it to "Game switch" or "Auto boot"? It has to be at "Auto boot" in order to boot from the harddrive, otherwise you disable the SCSI controller. Switch over when you have powered off the computer and drive, power up again and see if it makes a difference.