For anyone who runs into this same problem.
My NavigationAgent3D was updating its velocity but wouldn’t move. The velocity in the Y-axis was way bigger than the X-axis and Z-axis. I was spawning the Agent based on a position selected from the StaticBody3D/Quadmesh floor.
I finally figured out that I had quickly added a BoxShape3D for a collision shape to my prototyping game world’s floor. (which was just a flat quad mesh/plane) And the collision shape when added sits above the floor mesh.
So the solution was simply lowering the collision mesh so that the top of the boxshape3d sat just below the quad mesh. Navigation works.