I think I may have encountered a bug where your new drag cubes aren't properly checking whether a part is in front of them, so they're acting as if the airstream is directly hitting them even though they're in the middle of the craft. This only happens to parts placed after downloading the mod, the drag cube modifications go through just fine on existing parts.
See below:
https://ibb.co/5TNygy3
https://ibb.co/bL2dvKv
Not sure exactly why this happened, but if you need any more info on it I can try and get it.
EDIT: It seems the large cargo bay is giving me the "open" drag cube when closed as well.
https://ibb.co/BjGfgTt