Hi, thanks for giving my tool a try! If you're using single-color materials (i.e. no texture, just a flat color, and applied to the faces) then this should work (I use blender to make my models, and I have had no problem with this).
However, I don't think this would support vertex colors, sorry! Also, custom shaders aren't supported. I set my colors on the default blender material and these import correctly. If your custom cel-shader has a different format for the colors then I don't know if FlatPixel will be able to pick that up.
