My latest attempt worked, I now see a .faction file in my Factions folder. The only difference between this and my previous attempts was that I had Steam cloud sync turned off.
For the record, on my last attempt that didn't work and with this most recent one that did work, I chose the following:
Leader: Changed the foreground and background pictures, the leader portrait, entered a leader name and simple description.
Race Overview: Entered a name, short name, ship callsign, homeworld name, and simple description. Selected a race logo, chose Iridii as the star system. Did not customize the start up screen.
Traits and abilities: Chose Patriotic and Prolific, Productive(1), Clever(2), Content(1), Fertile(1), Courageous(-1), and Fast(1).
Appearance: Chose Iconian ship style, made no other changes on this screen.
Personality: Took the default Basic Tech Tree, Pragmatic ideology, selected Peaceful and Spiritual character traits, did not change any priorities.
Large map, loose clusters, Altarian/Drengin/Krynn/Thalan opponents.
I have Steam on two computers, however the second one is 32 bit so I don't have GC3 installed on it.