Dear @Lauren.Hall,
These values of ME=IMASS and CE=ISTIF are the rigid-body mass matrix (including full-system mass, center of mass, and inertias of the NREL 5-MW baseline wind turbine atop the OC4-DeepCwind semi) and mooring stiffness matrix, respectively. I would guess this ME would duplicate what you refer to as M in your equation of motion. And it doesn’t appear that you’ve included the body weight contribution to the stiffness, which is discussed in the following forum topic: Properties of NREL 5MW-OC4-DeepCwind SemiSubmersible wind turbine in FAST and reference.
Best regards,