No bug. You probably should've asked this in the "Shaders" forum. Post-process effects only act on images -- such as the bmap generated by a view, so NOFLAG1 on a PROCESS_TARGET view is useless.
I think there are two ways to approach this:
1. Do the toon effect in the object shader. No post-process -- when you are in thermal mode you set the camera's material to Thermal_mat or wahtever, and have a material event (ENABLE_RENDER) that sets material skills (for colour) based on each entity's own skills. The main disadvantage is that if you want the toon effect to take into account things like shadows, specularity, and transparency, the one shader has to handle this for all different material types. In practice this may not be noticeable to a user in thermal mode, and if you think about it will not matter for something like a thermal view.
2. Post-process white toon effect, but multiply it by a colour map that will make some parts red and some parts blue. You'd either need another view for this (this could be quite bad for your framerate) or, since most cards these days support multiple render targets (MRTs), just have each entity's shader output a red colour or blue colour to another render target. The disadvantage here is either speed (the first case), or having to modify every shader to use MRTs and output a colour (the second case).
1 is ideal, IMHO.
Jibb