Go into Content Manager and ensure that you have nothing open for edit. This will prevent your assets from appearing in a route. Also check for missing dependencies. You'll have a Yellow gear for missing items and a hammer and screw driver for open items.
Commit any open items by highlighting them and pressing Ctrl and M at the same time. Missing dependencies will require downloading parts off of the DLS.
Now if your route does not show up in Trainz its self, you will need to clear the yellow star at the top. This is the favorites, and by clearing this, all the routes will show up, and not the built-in ones.
John