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)
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
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