There could be at least two things at play. First, the relaxation is carried out with periodic boundary conditions (equivalent bulk), but the forces computed with open (two-probe). On the one hand, since the methods are a bit different, different forces can be expected. Also, you mentioned that you have constrained some atoms in the optimization (which is natural), so the system is not completely relaxed. Also, I would generally be cautious to trust the absolute forces from the two-probe calculation to a high degree, but rather look at how they might change as a bias is applied, or some other change made to the system. Some improvements of the force calculations for two-probe systems can be expected in upcoming releases of ATK.