Rich,
I am quite a rank amateur on this, but two thoughts, from problems that I had. Maybe a simplification, but:
1) On the Viaduct yard to Upperby/Dentonholme, is your loco at the correct(south) end of the train?
2) When that train (Canal to No 11) gets to No11, it has to run round the train to return, via Lawson's Yard, to Canal.
3) I assume that you have brought the loco coalout of Upperby shed. Again, is the loco at the correct(north) end.
I feel, and there are many more experienced than me, that if your programme is newish, post 2004, that all bugs have been ironed out.
regards,
Tony Dale