The secondary consolidation (creep) calculations in Settle3D start at the end of primary consolidation. A primary consolidation of 100% only occurs after infinite time, and for this reason a default value of 95% primary consolidation is used as the starting point for secondary consolidation. This means that secondary settlement will only be calculated in the current stage if the degree of consolidation at the previous stage reached the specified value (e.g. 95%).
In determining how to set up your model, first understand that a stage represents a specific time, not a time interval, when doing time-dependent consolidation analyses in Settle3D. So the settlement occurs between stages. If you apply a load in Stage 1, primary consolidation will occur between Stage 1 and Stage 2. Since the earliest check for secondary consolidation is performed after some consolidation has occurred, this must be Stage 2. So the earliest secondary consolidation can start is Stage 2. Therefore there is no way to get secondary consolidation to occur between Stage 1 and Stage 2. Thus the reason why when doing an analysis with secondary consolidation it is important to use many stages during the primary consolidation phase in order to properly determine the time at which secondary consolidation kicks in.