In this paper, we deal with the handling of the electrostatic forces in complex molecular systems. In particular, we focus on instabilities experienced by reversible multiple time step algorithms when used in conjunction with Ewald summation techniques for periodic systems. We show that energy conservation is negatively affected by the intra-molecular energy term due to electrostatic excluded contacts required by the most frequently used of the modem force fields for biomolecular systems. These effects are due to a non-complete cancellation of the intra-molecular electrostatic energy and forces at intermediate or long time steps.