I don't know much about auto air conditioner's and heaters, but I'll take a stab at this.
Have you checked the air mixer mechanism? (Sorry for the laymens term. What I'm talking about is that mechanism that allows it to mix the cool and warm air.)
If that isn't the problem, check the relay that is in between the control knob and the air mixer mechanism motor. That relay may be going bad.
I'm sorry if I'm no help. As I said, I'm excellent at house-sized (residential) climate-control units for my age (13 years old), but terrible at automobile climate control equipment. Both are so different yet the same.