I've experienced something similar when wearing my jacket and Cap2's in my sleeping bag…sure my core is more or less warm, but the bag interior and the air inside the bag feel cold. With this, since I don't carry down booties or gloves, my hands and feet are cold. I have discussed this with some fellow hikers around the campfire and one theory is this: having my body core covered and insulated prevents that area of my body from warming the rest of the sleeping bag. Those areas (core and legs) contribute very little to warming up the bag and thus the inside of the bag "feels" cold. My feet, hands, and neck will be cold in these consitions unless I also add insulation to those areas. At this point, with all my body covered by a similar level of supplemental insulation, I can then sleep comfortably below the rating of the bag. In my case, not sufficiently insulating my feet will doom them to be chilled by the cool air within the bag. Someone went as far as to suggest I was better to not wear any insulation to bed, thus allowing my entire body to contribute to keeping the interior at least somewhat warm.
If this theory is at all valid, the take home lesson would be, if I'm going to wear extra insulation to bed, I should make sure I can add a similar layer on all parts of my body. Time to carry the booties and gloves if temps might dip below the bag's rating.
What do you think? Make sense?