The clock stops if you change to a different status where the clock does not apply (for instance, student). In these cases, the clock will resume as soon as you acquire any of the affected types of status. It also stops if you leave the USA, even for a short trip. In this case, the clock would resume when you return to the USA in H-1B status. Of course, if you leave the US for one year, then the clock would also be reset.