The idea is pretty simple: In the rest frame there is one event, box radiates energy. After the box radiates energy its mass has decreased. In the moving frame there are two events separated in time and the box has three different values of enegy.
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Last I heard the box was gaining energy, now its losing energy? Oy vey! Anyway, so far we've just been arguing about what constitutes the box and what does not constitute the box, and clarifying the issue that if the box gains energy, it gains energy because of some transaction with an entity that is not the box that is losing energy. The rest is accounting details which revolve around what constitutes the box "now", and exactly when we make the bookeeping transaction that deducts the energy from the "non-box" account, and adds it to the "box" account, or vica versa.
Think more about simultaineity.
Pete
In the limit as the size of the box approaces zero, the difference in simultaneity approaches zero, and it becomes a non-issue. This is one of the reasons the approach of describing a system in terms of a stress-energy tensor is very useful. All the trivial accounting details disappear, and one can concentrate on the physics.