Entities from spawners with custom data tags not recognized by commands

An entity with custom data tags (ex. Leather armor, Invisibility potion effects) that is spawned from a spawner does not respond to commands, specifically the /kill and /execute commands. Strangely, this does not occur with any entity not spawned with that spawner.

When I ran the command "/kill @e[type=Zombie]" I expected all the zombies in my world to die, including my customized zombies.

Instead, only the naturally spawned zombies/zombies from spawn eggs and custom zombies from command blocks were killed, while all of the zombies with custom armor sets, custom names, and potion effects that had been spawned from the spawner remained in the world. After running the command, I received the message "That entity cannot be found"

I ran the command again, only to find the same result. After several tries, a few of the zombies responded correctly, but most still ignored all commands that would otherwise affect them, such as /execute.

Steps to Replicate:

1. Use the /summon to summon an entity with custom data tags. (ex. "/summon Creeper ~ ~ ~ {Fuse:1}" )

2. Turn the existing entity into a spawner via third party tools (I used MCEdit version 0.1.7.1.win32 with Sethbling's "Create Spawners" filter. )

3. With the spawner created, spawn a few of the entities using both the commands and the spawner.

4. Run "/kill @e"

5. The entities from the command should have all been killed, but any entities from the spawner will simply give the message "That entity could not be found" in the chat.

Exact Steps to Replicate my Setup:

1. Paste this command into a command block and power the block:

/summon Zombie ~ ~ ~ {CanBreakDoors:1,CustomName:Nightbringer,CustomNameVisible:0,HealF:20,DropChances:[0.0F,0.15F,0.3F,0.0F,0.0F],Equipment:[{id:},{id:348,Count:1,tag:{}},{id:50,Count:3,tag:{}},{id:299,Count:1,tag:{display:{color:0,},}},{id:397,Count:1,tag:{},Damage:1}],}

This should spawn a zombie with a wither skull and black leather armor.

(1.5: You may want to spawn two zombies to compare later)

2. Using 3rd party tools, add Invisibility 1, Speed 2, and Jump Boost 5 to one of the zombies, and convert the zombie into a monster spawner. I used MCEdit version 0.1.7.1.win32 with Sethbling's "Create Spawners" and "Add Potion Effects to Mobs" filters.

These can be found here:
MCEdit: http://www.mcedit.net/windows.html
Sethbling: http://www.youtube.com/user/sethbling?feature=watch

3. Ensure that the surrounding area is dark enough for the zombies to spawn.

4. After both the custom zombies have spawned and naturally spawned zombies have appeared (Spawn eggs also work in place of natural spawns), run the /kill @e[type=Zombie] command. This should kill all naturally spawned zombies, custom zombies spawned with the /summon command in Step 1, and zombies from spawn eggs, but some or all of the zombies from the spawner should not respond to the command.

5. Run a /execute command. I used

/execute @e[type=Zombie] ~ ~ ~ detect minecraft:glowstone 0 ~ ~-1 ~ /fill ~ ~-1 ~ ~-1 ~ minecraft:air 0 destroy

. This should not work on the custom zombie, but destroy glowstone underneath any zombie that did not originate from the spawner.