Ah, it appears that Lua is saving things that it shouldn't. I thought I could avoid reconstructing the data every time I fix a bug, but it appears that it saves functions as well, if the objects contain links to them. This only shows up for the diligent players, who saved a game with 0.4.0 and loaded with 0.4.1. Update to 0.4.2, and everything should be work again.