I ran another scenario with and had a similar problem with the task vanishing.
RW2 noted four tasks in the drive menu (screen shot 1). However, the starting station showed the start and the next task as one task (screen shot 2). The game did not show the go via task (screen shot 3). Once I left the first station, the go-via task was left (screen shot 4).
Screen shot 5 shows a discrepancy between the task (go-via) and the debug (which shows a StopAt, presumably at Norwood Yard). Once I passed Streatham, the task vanished from the task view and the debug menu remained the same (screen shot 6). Finally, if I set task id 2 as successful, then it showed the end task of the scenario as the next task (screen shot 7).
Please do not take the feedback as bad. I would like to use the tool more and like the sounds as well as the GUI. In fact, I want to replace the old GUI with the one offered by RW2.