Two robust fault detection schemes are presented to detect faults affecting the thrust system of the chaser spacecraft involved in the rendezvous phase of the Mars Sample Return (MSR) mission. The idea of both proposed methods is to transform the unstructured uncertainty caused by the electronic induced delays into unknown inputs and decouple them by means of an eigenstructure assignment (EA) technique. The first method utilizes a Cayley-Hamilton theorem based transformation whereas the second relies on a first-order Pade approximation of the time delay. The performances of the proposed schemes are compared by a sensitivity/robustness analysis campaign of 4240 runs within the "high-fidelity" industrial simulator provided by Thales Alenia Space.