Ok, just re-installed, and it remembered the settings - perhaps because when I did the uninstall, I said to not remove previous settings...?
Hope this helps someone else.
Yes, maybe if you used the forum search, you would see that is how it works - you uninstall Fences 1.x, but tell it NOT to remove the Fences and settings, and this will preserve them when you install Fences 2.x.