I was recently working on a character model, and I encountered a problem while using the Texture Paint mode. I unwrapped and assigned a texture to every piece of the model, and then went to the Texture Paint mode to work on it. When I finished the work I rendered it to check the result, and then I noticed certain colors of the texture didn't appear at all in the render. The flat texture and the model in 3D view look like this:
For further reference, I'm using Cycles Render, and used the node editor to apply several shadings and displacement. For the scene, I'm using two spotlights, both white in color, and black background. Also, while in Texture Paint, I used the Multiply and Lighten blends for adding contrast, and the Overlay blend for applying the purple hue. I'm using Blender 2.74.
Here is my node setup