Sounds like you have the exact problem Truefocus on the Hassy was designed to answer. Focus+recompose usually moves your focus plane by tilting the sensor-plane forward. It's not a question of initial accuracy, but that you're moving the plane of focus back by moving the centre of your sensor forward, and thus the field of focus backwards, just enough to impact sharpness.
If that's not the problem, you may have some serious alignment issue with your mount, AF sensor or focusing screen holder.
Good luck and love to know if you can fix this.
- N.