Kickstart 3.1 waits about 30 seconds for IDE drives before it starts scanning the other devices.
If this is not your problem, you probably had something installed on the IDE drive that is needed to read the SCSI drives. Probably the SFS or PFS3 filesystem. Hold down both mouse buttons after reset, then disable all SCSI partitions in the early startup menu and boot from floppy. Use HDToolbox to install SFS or PFS3 (whatever is needed) on one (or all) of the SCSI drives.
Bye,
Thomas