I've not tried playing with Victory Points, so this whole scenario is alien to me. Looking at the save, at the details of the setup, and the effects you are seeing, I'd hazard a guess that you've changed more than just the Victory Points limit. Changing that wouldn't have any major impact, as it's just a number.
I've tried playing the game for a few turns and nothing strange happened, but I'm really not sure what you were trying to do with it, so I very much doubt whether I repeated any of your moves.
Looking at your in-game Victory screen I see that you also have Instant Elimination enabled, with 1 city loss resulting in destruction of the civ. This probably explains the instant destruction of China. I can only theorise that the Iroquois survived by respawning their capital. If the zulu SOD captured one of your cities then that would explain why you died, though the absence of a declaration of war is strange. I cannot explain why you were gifted the Temple of Artemis and a leader.
I suspect you are right that you have set up some strange game conditions, but all these strange victory conditions mean very little to me. I still think you'd get better input in the main forums, where there are lots of players who have seen it all, done it all, and can advise whether what you are seeing is par for the course.
[PS] Here's a perfect example of what I'm saying. I posted this, looked at the RSS feed, and found a thread in the general Civ3 forums started by someone who had been beated to a wonder by the AI, even though they investigated and knew they were ahead the previous turn. One suggestion was that the civ may have got a scientific great leader to build the wonder, which happens if a civ is the first to complete a tech. Did your leader arrive as a result of completing a tech?