I have noticed quite a few people with only 1 train with the new skin, including 2 co-op mates (and myself, at first), so I think lots of people are confused.
You can add the new skin to all of your trains as soon as you get it, just do the same thing you did to skin the first 1 on the other 2...tap the station, tap the icon in the upper left, tap the train, tap the new skin, tap use.
Hope this helps someone! I wish we could talk to each other in the game!