Layers in materials required me to shut the project down and restart it to get it to display correctly under Target Layers in the Paint section. That is very bad and frustrating. Please fix ASAP. picture below shows there is nothing wrong in materials. It is a bug.
what it was was an inconsistency. the layer information had popped in without me using the apply button, but later when I added some texture samples they did not pop in automatically. restarting the project fixed this inconsistency, but simply using the apply button regardless appears to work perfectly well.