Hitting back after choosing a custom faction in a new game puts you into editing that faction instead of back to faction select (so you then have to exit faction editing and go back to new game).

Seems like any 'Empire' custom faction's tech research is completely broken. At least that is the only pattern I can see. I advise against making them for now.

Loading a game will reset all custom factions to what they were when that game was loaded. Removing new factions, reverting any changes and so forth. They will no longer be reset when you restart though.