I logged out of the game and back in a little later when i noticed two things:
a) most of my items in the inventory had been rearranged and
b) one of the items was missing (yellow box)
i things this happened due to the rearrangement of the items. i still had the required 4 free slots for the box that disappeared but these 4 slots where not in a 2x2 form so the box didn't "fit" into my backpack anymore and got "dropped".
the box was not on the ground when i logged in.
Same happend to me with my medical box.
And twice with a pistol.
Edit:
ID 0002666,0003854 and 0003793 are the same problem.
I have experienced this same issue. It seems that, on load, the backpack inventory is filled from the top down. When the items are dumped in (on load), sometimes larger items don't fit because of the way the items are organized. I noticed this happening most when I reorganize my backpack inventory so that empty slots are at the top (4-slot items on the bottom). When I log out and back in, items are reorganized so that the empty slots are on the bottom of my pack. Maybe it is my placement, but I always seem to lose my medical pouch. :(
Closing as duplicate of more recent but more popular report.
Please refer to #0008070: Backpack Item Rearrangement Upon Log out / Log in