Same issue for me as well. I had 4 to 5 chests full of resources and after saving by going to menu or exit saving, all chests get emptied. however your inventory stays the same. As a workaround, if I save, I move as much as I can to inventory first. This definitely need to be fixed. Also, anything in the nets disappears as well, but that is tolerable.
Edit - Using Windows 10 and the 64 bit version 1.04.