I got this response from Joel Slagg about your problem. Bob Parrish is also one of our local experts. See his previous post.
I believe that in Ship-It, interchange tracks only operate between divisions. I have a somewhat similar situation to the one described in the question, involving the interchange track at Rome on my layout. I had to put the town of Rome and all of its industries (except the interchange track) in a separate division. The interchange track is in the main division along with all the rest of the railroad. Mainline trains do not switch Rome, but they do switch Rome Interchange.
I set up two switch jobs which I call the 1st Rome Switcher and the 2nd Rome Switcher. The first one is scheduled to run before any mainline trains get to Rome. It runs from Rome to Rome Interchange and back, and its function is to move cars from the industries to the interchange track for later pickup by mainline trains. The second switch job also runs from Rome to Rome Interchange and back, and it is scheduled after all mainline trains have passed through Rome. It distributes cars from the interchange to the industries at Rome, and also frequently respots cars from one industry to another at Rome.
Once I figured out that it was necessary to have two divisions to make the interchange work, this was all quite easy to set up and it's working very well for me.
Hope this helps,