Drusim: Hi Gaunathor, It was a mining ship that went missing early in the game, just after I'd finished mining an asteroid belt. I'd say probably about an hour into play.
Mining ships can occasionally be hard to see on a mining base. Especially when the camera is fully zoomed out. However, it should still be listed in the Planet / Ship List. If it is not, then the only other option is that it got destroyed by an enemy ship. In that case, there should be entry in the Events tab of the Civilization Manager. If neither is the case, then I'm not sure what could have happened. I never had a ship simply vanish on me before, and I've been playing for over 12 years now.
As to the other issue/bug, I was playing as the Terran Alliance, I didn't customize anything, I just changed the name of my leader and civilization. No revolt or secession occurred, this happened early in the game as well, I'd say maybe 2 or 3 hours in.
Okay, those were the only two possibilities I know of, that could have caused this through regular means. There is another one, but that would require that you activated cheat-codes. One of the codes allows you to "hail" yourself. Basically, start diplomatic interactions with yourself. You could have accidentally pressed the button-combination.
If that's not it either, then I'd really like to take a look at your save-game. I definitely can't promise a fix then, because it could only be a bug in the engine, and I don't have access to the code. However, there is still a slight possibility that I might figure out what caused either of these issues.
Bookwyrm627: Hello Gaunathor! Nice to see you still poking around this game; I remember your name (and avatar) from the GalCiv2 forums (though I only lurked, never registered). :)
Hi Bookwyrm627! I only recently returned to GalCiv 2 actually, after having some rough years. Right now, I'm working on another version of my mod, Autumn Twilight. Should be out in the next couple of days. Just finished the documentation, but I still want to run some test-games before the release.