I've run the four passenger scenarios in East Coastway (and somehow got a trophy for doing five, even though I've only completed four). Now one of those is next on the Journey list, and it's not checked as completed even though I have a score and the gold. Do those two game "areas" not overlap? And will that also apply to the timetable services?
When you do Scenarios or timetable services from the Journey list, it will also count in other lists, but not in the other way. So maybe finish the Journey first if you want to complete the list, unless you don't mind doing the same thing twice.
When I did IOW, I did all the journeys, but the scenario ones didn't count towards the trophy, and I had to re-do them on a new profile, from the Scenario menu. IOW was the only one it's done that on (at least for me)