I think the confusion lies in what 'temperature' is. Temperature is the average *kinetic* (motion) energy of a system. As the system cools, the total kinetic energy in the system drops to zero. But this is talking solely about objects as complete entities (ie: atoms as atoms, electrons as electrons when they're freely moving on their own, etc). So even if you could cool an atom to absolute zero - that would merely imply that the atom is completely stationary (in its local frame - I really don't want to get into relativity here :) ). The movement of its electrons, protons and neutrons do contribute to the kinetic energy of the atom as a whole.
However, even THAT is a problem. Because of quantum mechanics, you cannot know both the position and momentum of a particle with infinite accuracy. If your view of absolute zero were correct - you'd know both exactly (you'd have its position since it's not moving - and you'd know its moment perfectly - it's zero) - which would violate Heisenberg's Uncertainty. In fact, if you could stop a particle (reduce its momentum to zero), it's position would infinitely indeterminate - it would spread out until it's a little bit everywhere. Conversely, if you can hold it in one place, it would gain an effectively infinite momentum which would allow it to escape by tunnelling.
But neither of these things are caused by changes in kinetic energy so they can't be considered 'temperature' in any normal sense.