You know, I had the same problem the first time I ran through it. Once I removed the quest from my mission log I realized I was looking at the wrong mission terminal. I think there are two - one across from the other. For example, if you are facing forward and going to the one on the right, try the one to the left instead. I'm hoping that helps - if not, sorry I'm at a loss.
EDIT: Also, try right clicking on your character picture and choose to reset all phases (of flashpoints).