I got a theory, does the departure time in the route system change when the departure location time change? I think my flight is departing at the DST time and is now departing at the non-DST time. Eg. it was departing at 10am DST (landing at 1PM JST) and is now departing at 10am non DST (meaning 11 DST time, and arriving at 2pm JST).
Have a look at the route that isn't working. Both are scheduled so that the second leg starts as soon as the turnaround is complete.
Have a look at the route that isn't working. Both are scheduled so that the second leg starts as soon as the turnaround is complete.