OK, having a bout of Deja Vu tonight. My Amiga refuses to boot up (just getting a blank screen) so I used the new startup tracking feature to step through each command.
If I skip the setpatch command the Amiga boots, albeit in reduced colour mode. If I enable it - it fails to boot. This is why I had commented it out originally.
I have tried going through each command in the startup-sequence and the only odd thing I can find is when it loads 'IPrefs' a system requester pops up to reset the screen and then the whole Amiga locks up completely (requiring a reboot).