If you include potential energy along with the kinetic energy, then you must exclude from the net force, the force that is associated with the potential energy. In your situation, if you take "net force" to mean the sum of all forces except gravity, then the work done by that net force equals the change in the sum of kinetic and (gravitational) potential energy.
To put it more precisely, there are two kinds of forces: conservative forces, which have potential energy associated with them, and non-conservative forces, which don't have potential energy associated with them. Define the mechanical energy as the sum of kinetic energy K and the potential energy U:
[tex]E_{mech} = K + U[/tex]
Also define [itex]W_{nc}[/itex] as the net work done by the non-conservative forces only. Then you can write the work-energy theorem as
[tex]W_{nc} = \Delta E_{mech} = \Delta (K + U)[/tex]
In this version of the work-energy theorem, the effects of gravity are included on the right side of the equation, via U. [itex]W_{nc}[/itex] does not include work done by the graviational force.
In the original version of the work-energy theorem,
[tex]W_{net} = \Delta K[/tex]
the effects of gravity are included on the left side of the equation. That is, the work done by the gravitational force is included in [itex]W_{net}[/itex].