In ArcScene, when a vector layer uses a raster as a source for its base heights, the base heights are calculated based on the maximum resolution of the raster. When a raster is set to its own base heights, the raster is 'down-sampled'. There can be a mismatch between the z-value of the surface and the draped vector.
It is possible to use the maximum resolution of the raster, for its own base heights. Use the Raster Resolution button on the Base Heights tab in the Layer Properties dialog to changes its resolution. However, be aware that the higher the resolution used for the base heights will decrease the performance of ArcScene.