there seems to be a bug where almost every chest in the Pneumatic craft buildings or smelteries are always empty, the other buildings seem to have stuff but I've check about 20-30 of the pneumatic craft and smeltery buildings and not one had any items.
You can break the blocks/parts from those mods in those buildings, same with the bigreactor parts in the reactor buildings.
What's the chat saying when you open a chest? Is it possible that you was already there and looted this chest? Everyone has it's own chests and the chests get only reset if you die so it's possible you looted this empty chests already. Only the blocks (seared blocks, pneumaticraft parts etc.) will be rebuildet after an hour, not the inventory of the chests. Also there is a random selection of the content so it's possible that a small amount oft chests only contains junk and very very rarely they can be empty.
it doesn't have the message "you've looted this treasure already" or whatever it actually says, it normally says something along the lines of "You've found treasure."[DOUBLEPOST=1409201662,1409184589][/DOUBLEPOST] this is how almost all of them look to me.
I am also having this problem, I think I looted one chest in smeltry building and now all other ones I open give nothing. Edit: Now I'm finding stuff in chest, I don't know what changed.
