Swapping materials before and after a scene Capture

How are you calling this function? Using Editor Utility? This seems to work for me:

Don’t forget to turn off the capture every frame option.

Are you sure you don’t want to use the heightmap to generate a normal map? There are fully functioning algorithms for this out there. Since you’re already dependant on the render target resolution, you could use a high-res landscape to paint on, then use a second lower-res landscape to apply everything to, for later use.