Bug:
Sometimes when an item is picked up it replaces the boots/boots slot. thus deleting the item in that slot.
(You can't see the items in F5 mode)
When throwing boots/legging/chestplate or a helmet it is places the item one item slot too high (helmet chrashes the client)

Repreduce:
We always got the bug when on a Vanilla 1.4.6 server, when pressed (CTRL) Q and 0 of that items in your inventory

This still isn't solved: https://mojang.atlassian.net/browse/MC-4560

Edit:
This seems to be the CanPickUploot in the player.dat file or level.dat. for some reason this is randomly set to one for players on our server with pure vanilla

on a zombie the first slot is the item slot and the second the armor boots slot, this explains why it put an item in your boots item slot