I'm trying to clean up a model and have got it primarily finished except for one thing. I've run the Polygon Cleanup Tool in order to only select any problematic areas. I have some faces that were selected with the Faces with zero map area option. In order to make sure that these newly resulting faces were mapped I ran Automatic Mapper on them, then placing them back into their specific positions with the rest of the already placed shells.
After running the Cleanup Tool once again I still receive the same results. In order to check this I went back and used the Automatic Mapper once again, then ran the Cleanup Tool once more without moving the UV's . This actually results in no selected faces.

I've never come across this before so was wondering does anyone know of a reason why this is happening and what's the best way to work this problem out? Thanks.