BVE has an interesting hierarchy.
You should have a "BVE" folder inside C:\Program Files (x86)
Inside your BVE folder: C:\Program Files (x86)\BVE you should have a "Train" and a "Railway" folder.
The trains obviously go inside the "Train" folder. Inside the "Railway" folder, there should be another three:
"Route", "Object" and "Sound". You've got to make sure everything is where it's supposed to be in order for the routes to be working properly. If the objects and the routes are in two completely different locations, they will not work properly.