John,

I used to be troubled by the same thing, and as I continued to practice they eroded. Consider that when you’re sleeping, you’re not distracted by your senses, and experience the raw state of your mind more directly. That raw state has been fed and bloated by years of delusion, of self criticism and poor self nurturing habits. As you move toward mindfulness and health, the difference is much more noticeable. Your mind now intentionally moves toward joy, which will erode the underlayment of unease.

If you’ve started a metta practice, that knot of painful karma in the subconscious erodes quickly. Don’t bother giving it more gravity than it already has, it is only baggage, meaningless in and of itself, and you’re already taking the steps necessary for its uprooting. Namaste.

With warmth,
Matt