In a previous study, a mathematical model of heat diffusion in a temperature modulated differential scanning calorimetry (TMDSC) specimen was derived. The model considered the specimen to be of cylindrical geometry with top and side surfaces exposed to the block temperature while the bottom surface was considered insulated. Contrary to most other derivations found in literature, this specific model took into account both radial and axial thermal gradients within the specimen and did not neglect the thermal diffusivity of the sample. Previous numerical simulations with this model showed that temperature gradients of as much as 0.15 K can exist within a polymeric sample subjected to typical TMDSC conditions. In continuation of this work, the present investigation concentrated on assessing the effect of sample thickness on thermal gradients and time to steady-state. It also explored the influence of sample thickness on heat flow phase, without using a complex heat capacity of doubtful physical meaning.