Okay, I looked into this and this appears to be due to the part scale applied to structural panels. Some of those panels are scaled quite small and initially they are considered occluded by the drag calculation, but when the landing gear are retracted drag is recalculated and they are picked up by the drag camera and start contributing to the drag. This wouldn't be a problem if they weren't part-scaled, because they are quite small and would have a negligible effect on drag, but since they are part-scaled they are using disproportionately large amounts of drag. It would be like trying to fly this craft. I would recommend toggling off "Include in Drag" for those structural panels via the Tinker Panel.
Okay, I looked into this and this appears to be due to the part scale applied to structural panels. Some of those panels are scaled quite small and initially they are considered occluded by the drag calculation, but when the landing gear are retracted drag is recalculated and they are picked up by the drag camera and start contributing to the drag. This wouldn't be a problem if they weren't part-scaled, because they are quite small and would have a negligible effect on drag, but since they are part-scaled they are using disproportionately large amounts of drag. It would be like trying to fly this craft. I would recommend toggling off "Include in Drag" for those structural panels via the Tinker Panel.