When the route traverses several junctions, and the halts are very far apart, the intermediate stations do not get auto-populated. For example, in this case, if you look at the map, you will see a straight line between HYB and NZB.
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The solution is to insert a "Passes-Thru" station in between. In this instance, you may insert SC as a "Passes-Thru" station with the approximate time of passing. Then the map and kms. will recalculate. When you insert a Passes-Thru station, please remember to check the "P" radio button on that row.