Latest TC and Spigot. If a new world is generated, this doesn't seem to happen. Do the .dat files in the data/ folder have anything to do with this?

Oddly enough this seems to only be a problem for certain desert temples, since I found one with chests. I have tried completely removing the region file containing one without chests, and upon regenerating it, it still didn't have any chests in it. On another note, a player has told me that they found a blacksmith chest but that when they right clicked it it disappeared.