Peter,
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Maybe you've entered the same car twice, or you've used the hyphen feature to enter two identical cars into the database.? Can you please go to the Cars window after you've build both of your trains.? Use the sort by "Train" radio button on the bottom, and then search for car road numbers using the find box at the bottom of the window.? Let us know how many cars you find, and to which train's the cars are assigned to.
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