For example, if you're in the middle if a single-encounter skill challenge, you can't short rest in the middle to recover your encounter power.
An example of this is a tense diplomatic negotiation with the High Duke of Cantermoor. Tempers are at the surface, and you -need- to prevent war. This is a single encounter, altho it might last longer than five minutes.
During the encounter, you use an encounter power to give a boost to a Diplomacy roll. Because you cannot leave the encounter, you cannot take a short rest to recover it, even if each roll represents five or ten minutes of negotiation.
(However, there's nothing saying you couldn't ask for a brief recess in the middle so you can all take a rest. This would definately count as a short rest and you could recover your powers then)