Did you save the consist again after you rotated it? It sounds like the consist you're selecting was simply built facing the wrong way. The easy way to find out is to select the consist from the consist list and place it on the track. If the red arrow is at the front end then it's facing the wrong way. In this case you'll just need to change the train's heading by using the button with a green and red arrow on it, and then save again. Then you'll need to set up your portal with the new consist.
JB