When I go to a singleplayer world and spawn a tool/armor with meta data -30000, like /give mihko9 314 1 -30000 (to increase durability) and the rename it to anything, it will eventually disappear from my inventory when you move the item around your inventory and opening an furnace/chest/anvil/crafting table.
Steps to reproduce:
1.Open a world with cheats enabled.
2.Do /give username 314 1 -30000 a few times.
3.Rename all items(in this case golden helmets) to anything.
4.Randomly open/close chests/furnaces/anvils/crafting tables and move the items around your inventory and they should disappear.
Environment
Minecraft Version: 1.4.6
Operating System: Mac OS X (x86_64) version 10.6.8
Java Version: 1.6.0_29, Apple Inc.
Java VM Version: Java HotSpot(TM) 64-Bit Server VM (mixed mode), Apple Inc.
Memory: 979259736 bytes (933 MB) / 1069416448 bytes (1019 MB) up to 1069416448 bytes (1019 MB)
Closing this issue since it's now impossible to get something with a negative data value.