Markov models (MM) are widely used in dependability assessment of complex safety-critical systems. The main computational difficulties in using MMs are model size and stiffness. Selection of the solution approach (SA) and tools based on analysis of MM stiffness and complexity increases the assessment accuracy. This paper presents the safety assessment of nuclear power plan instrumentation and control system (NPP I&Cs): a two-channel FPGA-based reactor trip system with three parallel tracks on “2-out-of-3” logic. The MM was built using a multifragmentation approach and solved with several SAs and tools. The analysis of results shows few application problems: the importance of usability-oriented tool selection, achieving an accurate result, and supporting the results verification.