I have been playing the 3.1 opt-in. In my latest game I tried to build Paxton's Emporium, but someone beat me to it. Later I noticed it in the list of things I could build, so I built it. I ended up using some saves during this game to investigate how arable land and food are handled by races that don't use food.
While doing this I decided to look for the first Paxton's Emporium that was built. I never found it. I think this means that a race built it first, then decided to destroy it for some unknown reason. After it was destroyed it appeared on the list of things I could build. To test this, I destroyed the one I built, went to the next turn and checked everyone's list of what they could build. It was on every one of them. It was not there before I destroyed mine.
If the original builder did destroy it, the question is why?
I think there is something strange going on at times with the AI's decision on what to build. During a game in which I used the console command "soak" to automate the game, I watched a planet of a race and saw it build a factory on a tile one turn, destroy the factory and build a research lab the next turn, then destroy the lab and build a factory the next turn, then continue to repeat. It had enough accumulated manufacturing points to build the structures in only one turn. This makes me think that sometimes the AI gets caught in a loop. I don't know what it does to get out of the loop, if it does.
For the Paxton's Emporium problem, I plan to replay the game that had the problem. I made a save at the beginning, so I can start there. I had finished building the Emporium by turn 52, so it shouldn't take too long for the "problem" to occur. I also plan to save every 10 turns or so. I have autosave at 5 turns, so I should be able to get a save before the building race deletes it or whatever happens.
I'll update when I get any results.