So I "listened" on a different set of speakers and understand your point. That tone is when the gain is low and the amp volume is cranked. It creates that boxy / woofy almost clipping noise you are talking about. Lower the master volume on the amp and it will go away. If it is present in profiles, that is how it was profiled. Just my opinion because who knows what you are hearing.
Edit ***If you hear it with recorded vocals, I have no idea what you are talking about.