Gage that is pretty well what most of the studies I have read prior on the topic say - the Ford link Donna gave doesn't actually come out and say that though - they want you to think its all about the little lip they added to the tailgate of their new trucks ;-)
An article that suggests as you do its the bubble effect you described can be found at
Truck Test Digest - Tailgate Up or Down.
Most of the studies I have read on the topic also suggest that a tonneau cover will also improve the MPG and a hard one more so than a soft one.