Steve,
As Griphos says, if all of your third-party routes give you SBHHs there must be something in your TS2013 installation that's causing that.
How is your Kuju folder broken down, size-wise, between RailSimulator, RailSimulatorUS and RailSimulatorCore?
The Bay of Quinte route uses all three of these and it could be that your total Kuju folder is just too big.
Bob.