Path Painter does not alter the texture layers of the terrain in any manner. It just works with whatever was set for the terrain. If you have issues like this, that's very likely due to the shading tool you applied to your terrain.

For example, CTS users can find that their road textures are black. That is because the texture is not in sync with CTS.

Procedural Worlds have a video explaining the problem and the solution here (click on the link to look at the appropriate section of the video):