This is usually a problem that when you start your system all the feedback sensors will be shown as 'Unknown' and this is taken as 'Occupied' for the benefit of setting signal logic and LOGIX. As soon as any of the sensors change state then they will start to populate the sensor table as the correct state (which for the most part will be 'Unoccupied') and things start working.
As you have found the easiest answer is usually to run a train round to trigger all of the feedback modules to transmit their state to the command station.
Suzie Tall