Oh boy, this patch seems to be causing all sorts of problems. I had to remove ALL instances of UO from my PC, then reinstall. Couldn't even log in before that. Now, when I boot up UO using UOA, I get two patchers.
I'm afraid I've got no idea how to get your game settings back; mine turned up again when I'd reinstalled. But I'm sure someone who knows more than me will be along in the near future!