In this work we discuss the numerical challenges involved in the computation of the complex eigenvalues of damped multi-flexible-body problems. Aiming at the highest generality, the candidate method must be able to deal with arbitrary rigid body modes (free-free mechanisms), arbitrary algebraic constraints, and must be able to exploit the sparsity pattern of Jacobians of large systems. We propose a custom implementation of the Krylov-Schur method, proving its robustness and its accuracy in a variety of different complex test cases.