If you name an item in an anvil it doesn't stack either on the ground or in the inventory with items with the same name. Waiting or re-logging the world fixes this.
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If it is indeed the same issue as MC-335, then someone needs to go to the naughty corner for marking this issue as only affecting 12w49a (a version that came out long after that bug was fixed).
I did some extra testing. It seems like it behaves like this if you're nearby spawner trying to spawn a copy of the item with the same nbt properties every tick. I only did the later testing in Mincraft 1.4.5, but I would guess this is the behavior in snapshot 12w49a too.
Is it possibly the same issue as in MC-4236?
Thanks for pointing it out, this is actually duplicate of MC-5413.
Unable to reproduce. That issue was fixed in MC-335.