How to reproduce:
1. Create two identical armor pieces which use the attribute system
2. Wear one armor
3. You'll notice that the attribute has been applied. In the pictures, it is speed.
4. Hold the identical armor in your hand.
5. Move your hotbar selector away from the armor
6. You'll see that you'll lose your attribute, even though you are still wearing the armor piece.
This also happens when you die and keepInventory = true
Edit: This is fixed in Minecraft 1.6.1
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I used the scroll-wheel click to clone them.

Is this still a concern in the current Minecraft version? If so, please update the affected versions in order to best aid Mojang ensuring bugs are still valid in the latest releases/pre-releases.
It is fixed in Minecraft 1.6.1 now.
Did you put the same UUID for both armor ?
If you don't want that happen, try to change the UUID (one of them is enough), it should work fine.