I was quite wrong about my 'discovery' yesterday. It seems that Pylons are picky about the ceiling height of your sub/add brush- they don't dislike subtractive brushes at all, as I tested again and it turns out the real issue was the height of the sub and add brushes. If you have a floor and also a ceiling there seems to be minimum height requirement. Which sucks really that I couldn't figure this out sooner. I was left scratching my head until now.