I am now very, very confused.
I uninstalled all GC games.
I saved the custtom files I wanted to keep to a separate location and deleted the GC folders in My Documeents.
I reinstalled GCiv. I started it, set my options to allowed mods, etc., and shut it down.
I then started GCiv, downloaded some ships and a civ, created a random civ, started a game, saved the game, and exited the program.
At no point in all of this was a folder set created in My Documents for GCiv. So... where is my saved game, where do my mods go, and what the heck?!