Having mistakenly convinced myself I had found a fix (I hadn’t – I broke DX10 and FSX fell back to FX9!) the next step was to hook the DX10 Device Create.
I tried the reference software driver to see if it was an AMD issue in the card/drivers.
Exactly the same, although at a peak frame rate of 3 per second the flashing was less distracting!
Then I edited the airport to add some concrete and took a snapshot in Intel GPA – this resulted in in the taxiway and runway not overlapping – so the FSX logic for drawing the airport took a different route and so sidestepped the problem.
Going back to the original problem The Intel GPA tools can show the history of a pixel. Picking a light grey one on the runway we see that the runway draw in erg 176 didn’t update that pixel as it was Z-rejected – i.e the dark tarmac pxels was rejected as further away than the light grey pixel from the taxiway.
So it seems that the problem is z fighting between the layers.