I've got pfSense on watchguards at home and they are installed on CF Cards. I have had some wonky problems before with upgrading, but not with fresh installs. Auto Configure on the ports ALWAYS works and that way you know it is the right port being assigned based on the fact that it is the only active port. You mentioned that you copied the config from another appliance (or that is how I read that) I figured that was what was causing the problems. The backend Id's for the NICs may not be named the same from from device to device, so if you restore that section of the config, it may break it.
I would do the fresh install, with auto config for ports, and then use config restore, but selectively choose things like firewall rules and aliases. Don't overwrite the sections for networking and what not.
Hope that makes sense.