Hi Chris,
Welcome to the forums!
It sounds like your database is corrupt but don't worry as there is a fix for it.
1) Close Content Manager and TRS2006 if you have them running and wait a minute or two for things to settle down.
2) Open the folder where you installed TRS2006 and delete the following files. You might want to search for them as it maybe easier.
assets.tdx and assets.bku
3) Once these are deleted, reboot your computer.
4) Restart Trainz as this will rebuild the database.
Depending upon the amount of time needed, this can take some time to complete. When it's complete, Trainz will start up.
5) Close Trainz and go into Content Manager.
6) Go to the Faulty content tab, or search for faulty = true in the search.
There will be faulty assets. Don't panic.
7) Highlight the list by clicking on one and then pressing the CTRL+A keys at the same time.
8) With the list highlighted, right-click and choose "View Errors and Warnings" (You can also access this from the edit menu on the top-part of the screen).
Any errors there should disappear, while any left over will need to be repaired. We can help you with the errors should there be any. Usually content is easy to fix.
9) Close CM and go back and run Trainz.
In the future, remember to wait a few minutes after closing Trainz or Content Manager before shutting down or restarting your computer. The screen is closed, but there are things happening in the background.
On another note, and this is important too for route editing. There are sessions and routes. They are connected, but exist in two different parts. Sometimes what you do in a session will not appear on the route. You will notice this if you place trains in the session as they don't appear on the route. However.... stuff placed on the route will appear in a session.
And there's another thing related to all this. A saved driver session will not reflect any changes made on the route or session. So if you are driving along, notice things out of place, go back and edit then drive again, you'll still see the problems in the saved driver's session. If you are testing, it's best to just exit and come back because the saved driver's session is useless at that point in the process.
Good luck and let us know how you make out.
John