Orange,
Which Amiga and 3.1, and what drive type (EIDE or SCSI)?
The A4000D (EIDE) under 3.0 and 3.1 both delays built into the DOS for EIDE drives to spin-up. 3.1 is 30 seconds. 3.0 was just a bit faster. Using a SCSI controller and drive to boot does not negate the 30 second timer. There is NO-EIDE fix (by Matthew Frost) that involves jumping a 4.7K resistor between pin 39 and pin 3, and another 4.7k resistor between pin 39 and pin 5 (the effect is to tie IDE data bits 7 and 6 high). This fix removed the EIDE wait.
What actually happens has been disputed by others, but if you hold the hard drive, you'll sense it "power-up". This is only the drive starting, and coming to full rotation speed. The drive is now ready for access. The delay was programmed into the ROMS to allow slower EIDE drives time to power-up.
The A3000 had it's own hard drive (SCSI) issues. Setbatt addressed those problems, allowing you to configure hard drive time-out and Logical Unit Numbers (LUNs) among other things.