One method disclosed herein includes forming first and second gate cap protection layers that encapsulate and protect a gate cap layer. A novel transistor device disclosed herein includes a gate structure positioned above a semiconductor substrate, a spacer structure positioned adjacent the gate structure, a layer of insulating material positioned above the substrate and around the spacer structure, a gate cap layer positioned above the gate structure and the spacer structure, and a gate cap protection material that encapsulates the gate cap layer, wherein portions of the gate cap protection material are positioned between the gate cap layer and the gate structure, the spacer structure and the layer of insulating material.