Hi Jeff,
The car on the alternate track should go to the spur, not the yard.? Are you sure that's what happening?
To use the alternate track feature, you would only send cars to the spur, and the program when finding the spur full, should send the next car to the alternate track.? When the spur car gets pulled, the program should send any cars on the alternate to the spur.? You shouldn't use a schedule in any way with regards to the alternate track.
The correct way to use the alternate track feature, is to tell the program which track is the alternate for the spur track.? Then you're done.
Dan