Witouht being there to troubleshoot, my first suggestion to alleviate your problem would be to get a larger piece of heat tape for the bottom enclosure. Which piece of heat tape, top or bottom, does your temp probe monitor temps on? If your temp probe is regulating temps on the large piece of tape, it is possible that the tape is getting warmer faste than the smaller piece, and the smaller piece is staying cooler, thus keeping the enclosure cooler. Try putting the same size heat tape on both enclosures.