On the third floor of the starter dungeon, all the chests and coffins were empty and the magical springs were only water.

I watched a playthru of this area and they were all full. The coffin leading to the Daimyo was also empty.

Are these bugs or is it random? 

hmmm… did you use the premade party?

Maybe I have a bug where I package the master player A that’s already been “played”. I’ll take a look.