I think you misunderstand. I booted without SS, and ran setpatch (which is the first command in the SS anyway). After this, the machine wouldn't bot at all, so did not have an opportunity to re-run setpatch, or execute the SS, or any patches within it.
I've found out why it's working after reinstalling. Setpatch is no longer patching the kickstart version! The command in SS is just "Setpatch QUIET". The AmigaOS ROM Update is in DEVS:. It says it is patching with 44.something when I run setpatch. But after a reboot, the version is still 40.68 :-?
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moto