What is the actual method you are using for setting the balance? When you say 'the plane balances at the main spar' this is only helpful if you specify exactly how the balancing is done.

What size engine is actually mounted on this plane?

If you have a .40 engine mounted and if you mean when the plane is right side up you must feed in excess UP elevator to fly level and when the plane is inverted you must feed in excess DOWN elevator it sounds like the plane is nose heavy, meaning there is excess weight ahead of the actual lifting point of the wing. But I am assuming you are flying at normal operating speeds for that model.

If you are flying at a very slow speed then the excess deflection of the elevator is probably required just to angle the wing to make the wing produce enough lift to keep the plane level.