Chest entities can't be rotated in Factorio. That is just limitation in the game. So if chest is not square it will not allow blueprints to rotate if they have such entity in them. I could create a modding interface request for Factorio 2.0, but there is nothing I can do for 1.1.
I already created a hotkey to rotate blueprints with merged chests, but I can't guarantee it behaves how normal rotate would behave.
