Okay, I've managed to see the error for myself now. Here's what I've got so far:
1> It only crashed in a few of my test cases. 3 out of 10, by my count, but this might be specifically related to the number of civs on the map, since all of my test games were on Small (6-man) maps.
2> It doesn't matter whether you went through the Advanced Setup screen or not.
3> It's definitely not triggering any of my own code. The game is awarding the win through some other mechanism.
4> It's an actual Transcendence win, not a Science one. So the fact that the science victory was disabled doesn't help.
5> It's not consistently one civ over another. I managed to trigger it three times; the first two were both Napoleon, so I thought it might be something specific to France, and I started a game with France as one of my opponents, but this time it was Egypt who won. It might be linked to the player ID number, though; long ago, I noticed that the arguments on the SetWinner function were reversed on the Wiki. So if victory ID #4 (Transcendence) is being somehow linked to player ID #4... obviously this shouldn't happen, but we're well past the point of arguing how things SHOULD work.
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So here's what I'm going to do. Right now, the Transcendence Victory is in the database with no prerequisites; it's purely awarded through Lua, which is why it shouldn't have been possible for this error to happen. So it's possible that the game is thinking that in the absence of an actual victory prerequisite, a random civ has met some sort of unset requirement. What I'm going to try, tonight, is explicitly setting the project prerequisite count to 20. It'll still award through Lua, but I'm hoping that this'll prevent it from being completed any OTHER way. The downside is that it'll be like SS Boosters, where you can build it in multiple cities, with each counting towards the final total (but the transcendence process only starting after the first is created).
Actually, that's kind of a nice idea: I could bump the number needed up to, say, 50, and cut the cost of each way down. The counter would still increment by itself, at 1 per turn, but you could hurry the process a bit by using more of your cities for building ascendance projects instead of building units to defend yourself (since the perma-war part will stay in). This does fix one conceptual problem that I'd had, which was that if someone beat you to the project by 1 turn, you'd never be able to catch up to them and could only try to eliminate them entirely within the 20 turns. This way, it'd still be possible to overtake someone if you had an advantage in number of cities and/or destroyed some of THEIR core cities. (I will NOT, however, make you have to shuffle units around like the SS parts.) Of course, this is generally academic, because I've never had a game where it was still competitive even into the Nanotech Era, but the concept is sound.
Anyway, I'll try that tonight and see if it fixes the problem.