Using Rigidbody and NavMeshAgent at the same time

I have a unit that I am hovering in the y axis using Rigidbody.AddForceAtPosition. The units movement (x and z axis) are controlled by a deterministic physics engine called DPhysics. I want to use Unity's path finding and local avoidance. When I attach a NavMeshAgent to the unit along side the Rigidbody the two conflict making the unit jitter and bounce which in return no longer hovers the unit.

How I can disable NavMeshAgent from effecting the y axis to allow the Rigidbody to work? Currently I disable the NavMeshAgent on Start and then when a move is ordered I enable the NavMeshAgent, CalculatePath, disable the NavMeshAgent and proceed with the movement of the unit. This seems to work for path finding (going from point a to b) but I do not think it will work with unit avoidance since the NavMeshAgent will be disabled when the unit is stationary.

Any ideas would be greatly appreciated.