If you transformed the blockreference by means of transformations that reverse the directions (like mirror transformations), they look different because now their normals point toward opposite directions.
The correct approach is to create two different instances of the entity, apply the transformation to one of them and to put them inside two different blocks of entities.
It is like when you design a house. There are the right handle and the left handle symbol definitions. Then, you insert these two distinct symbols with different position/rotation many times in your drawing.