On page three of the rules, it says (emphasis added by me):
When building track, points are awarded as follows:
* One point when a line connects to a national rail station.
* Two points and a branch token when a line connects to a Terminus.
* Three points when two connection stations showing the same Symbol are joined using one line.
* One point for each station contained inside, but not part of, a loop created by one line.
From this, it seems clear to me that blue and green stations count when scoring loops.