I recently got a new computer and downloaded Tane as well as TS12. While running TS12 I have routes that are listed in CM v3.5 but don't show up anywhere once I launch Trainz. What did I do wrong???
That's unusual in that case. I notice though that you mention Content Manager 3.5, so you may need to patch at least as far as 49922 (v3.6) or equivalent.