not sure if this helps or not but i've been having the same problem
when i start a new game and put down chests they store everything fine
if i leave the game and then load back into it i find the first chests i put down store everything fine
if i put chests down after reloading the game those are the ones that are not saving my items
still not fully tested it but i feel if you just manage to make a massive chest room before exiting for the first time then hopefully you'll have chests that save your items