Sorry for taking so long, but I have been away for a while.
It is possible that you have a totally difference issue.
As I understand it, there is a read-back for CANmessages sent out.
If the read-back does not happen, then the outgoing messages do not get cleared out of the transmit buffer. So, it is quite possible that your hardware is not successfully sending out the messages. This could be due to a hardware issue. In your simulation environment, the most likely issue is with termination of the CANbus. In a car, the CANbus termination is done by the car. As a result, scan tools do not have to deal with termination. Have you designed termination into your hardware? One way to know for sure would be to probe the CANbus with an oscilloscope to ensure the messages are actually going out onto the CANbus and that the signal is clean.