The problem is likely with the fact that importing any content into TRS2006 leaves it open for editing, and not in the game. You then need to accept everything as if you had just edited it. As mentioned, this is on the Monorail Information thread, as are a number of answers to problems others have had with the project, TRS2006, and Trainz in general
I'm glad you're interested in it all, but some people do have trouble getting it all in the game and working. As you might expect, it makes more changes to the original game than just producing a new type of standard trains vehicle.
Good luck, I hope you get it all running.
JFE.