Roger,
Does the normal CAN communication works on your board ?
I mean if you take the CAN example, compile it and then use a standard CAN viewer can you see the messages from the board/processor coming to the CAN viewer ?
This will validate that the CAN port works correctly. Try this at 500kb CAN speed. It that works, then user any other example project that has no CAN initialization inside and with the workaround proposed in that thread at 500kb it should work. That workarround is only for 500kb CAN speed in both Simulink and Freemaster.
FYI, the Freemaster and standard CAN messages can't coexist over the same CAN port.
Hope it helps!
Daniel