Custom Mob Spawners will first spawn unedited mob, then the correct mob.

Confirmed in 13w39b

Confirmed for 13w39b. SpawnData has not been removed: the game still requires it when loading a spawner's data. However, it does not save SpawnData anymore, nor does it load it from /setblock. It will load SpawnData if a spawner had it in a previous version, but after saving, it will be removed from the spawner, causing the observed issue.

SpawnData is not the same as Properties: SpawnData indicates the next mob to be spawned, just as EntityId indicates the ID of the next mob to spawn and isn't made redundant by SpawnPotentials.Type. The SpawnPotentials.Properties compound isn't enough to describe a spawner, as it's a list of random choices: the spawner needs to know what mob it's supposed to spawn next, and that's what EntityId and SpawnData are for.

This is why it is a bug for the game to not save SpawnData: it's a property the game still uses and requires; it's an error for that data to be stripped from the NBT, especially considering the game still reads the data when it is available.

Confirmed in 13w39b.

My spawner was a simple zombie one, but they had stone sword and iron plate included, the first zombie spawned had no armor or weapons at all, 2nd zombie and so on were properly equipped though.

This issue also happens for me.
I use hundreds of villager spawners for proximity detectors.
All are set to spawn with zero health at specific co-ords.
The first villager spawns nearby randomly with full health (similar as reported above) and the subsequent spawns are correctly spawned.

Confirmed for 13w41a (and b)

I can also confirm for 13w41b. Can this please be updated?

Confirmed for 13w42a and 13w42b.

Confirmed for 1.7 prerelease. You can test it with the following command:

/setblock ~ ~1 ~ minecraft:mob_spawner 1 replace {EntityId:Item,SpawnData:{Health:5,Age:0,Item:{id:7,Damage:0,Count:1}}}

Reload the world, and observe carefully: its first spawn will produce nothing (you must have particles turned on to observe the empty spawn) and subsequent spawns will produce bedrock. Consistently happens with reload.

Perhaps a better example:

/setblock ~ ~1 ~ minecraft:mob_spawner 1 replace {EntityId:Sheep,SpawnData:{Color:10}}

After every reload, the first spawn will be white sheep. Subsequent spawns will be the correct color, purple.