@Thomas
No I don't think that's it, my boot partition is only 1.2gb. The rest of the drive is a single partition of about 6.5gb. Could that cause a problem? Even with 3.9?
@Doobrey
No patches, it's a brand new install of 3.9. And yes, it's a real 3.1 ROM. I booted with no startup-sequence and typed in "setpatch SKIPROMUPDATES=ALL" and it rebooted and started up fine. So I copied the AmigaOS ROMUpdate file from my OS3.9 install disc, powered off and cold booted. Well whaddya know it worked :-D
-- EDIT
Well this is weird. After I copied the ROMUpdate from the CD over the copy in DEVS: on the hard drive, it booted up fine. I then cold booted and the error came back :cry:
I then booted from the hard drive with no startup sequence and copied AmigaOS ROMUpdate back to DEVS: and also to another file called DEVS:romupd. I then added the following line to the startup-sequence, just before setpatch:
copy devs:romupd "devs:AmigaOS ROMUpdate"
It now cold boots without a hitch every time. So it would appear that something during boot is damaging the ROMUpdate file. I can live with this now as I have found a workaround, but I'm a bit worried about what could be happening.