Hi dlmann,
Using conventional D-Meters, it is impossible to get accurate thickness measurments through coatings because the thickness of the coating becomes part of the thickness measurement. You are most likely getting your thickness reading error from the 12 mil thickness of the external coating. A simple mockup test panel will prove this out. Using a .375" steel plate, coat one side duplicating the exterior coating (material and thickness). On the opposite side, mask off one half of the surface and duplicate the internal coating (material and thickness) on the other half.
The method used to take thickness readings through coatings is called peak-to-peak or multiple echo. This technique uses at least 2 high amplitude multiple backwall echo signals and 2 gates to trigger the measurement. Typical transducers are single element delay line types. The contact face helps to dampen echoes from within the coating layer.
Most manufactures offer equipment that has this feature. Krautkramer's DMS (now discontinued) was a early machine that also had a A-scan display (for signal verification) and a data recorder.