OK, Al, let me restate in a more comprehensive manner and see if that helps.

We know that "dynamic pressure" is actually measured by the increase it causes in localized static pressure. So the term  "dynamic pressure" is actually just referring to the energy potential (Kinetic) of the moving air to cause a localized increase in static pressure - if  that air movement were brought to a stop.

 In other words, if we had a flow of air with a specific velocity and specific density, that air would have a ambient static pressure (say at sea level of 29.92" HG).  The moving air would also have a static pressure potential (Dynamic pressure) based on its velocity and density.  So that if a tube were used to measure this "Dynamic Pressure" it must first bring that part being measured to a stop the action of which converts the dynamic pressure potential of the moving air to a localized static pressure increase in the tube. 

 So the total static pressure at the measuring point would be the static pressure of the ambient air (29.92"HG) plus whatever increase was caused by stopping the moving air or converting its dynamic potential to static pressure.  So Pt = Pa  + Pd with Dynamic Pressure component, Pd = p*1/2V^2.

So in case of a duct there is, of course, only ambient static pressure in the duct if there is no air flow through the duct.  Once there is airflow then you also have potential pressure in the form of the kinetic energy of the moving air.  So that Pt = Pa + p1/2V^2.  p being air density, V being the velocity.

 The streamline duct (theoretically) can convert 84% of the moving air potential dynamic pressure to static pressure increase.  So that at the widest part of the duct just before the core you would have a total static pressure  Pt = Pa + 0.84*p1/2V^2. 

But, using differential pressure gauges with tubes pointed into the moving air, we are not measuring total pressure, but the pressure increase due solely to the moving air.  In other words, if you were measuring 5" H20 and then the air stopped moving , the gauge would read zero.

 So with the manometer you are measuring the pressure above ambient pressure or that resulting solely from the dynamic pressure potential of the moving air being converted from kinetic energy to static pressure.  Yes, the ambient pressure is present but you are not measuring it.  With no moving air the water levels in you manometer would all be exactly at the same level..

The fact is that you are measuring static pressure at both locations - the 9.5" before the duct was a static pressure increase in your measuring tube - cause by stopping the moving air so its refer to as dynamic pressure.  The fact is that you were also measuring static pressure 3.25" at the location in the duct - but both resulted from the transformation of the air's kinetic energy into a local static pressure increase.  Therefore, the fact that you were measuring considerably more pressure before the duct than inside it indicates that the air stream's velocity is not being efficiently transformed into static pressure in the duct.

This implies that perhaps there is less air velocity entering the duct than your measurement a couple inches in front suggests OR there is sufficient eddies and adverse flow situation inside the duct that precludes the efficient transformation into a static pressure increase. 

I do not have an aerodynamic or gas dynamics background, so I could certainly be wrong.  But, that is my understanding based on the somewhat extensive reading I have done.

Ed