Do you have a volt meter? In netural with the kickstand down, turn the key on and probe the Black/Orange wire going to the right switch pod. Should have 12V. If it does, then the interlock system isn't the issue. Basically, 12V here shows the system is energized. The starter relay then has two switches, the starter switch on the hot side and the clutch switch on the ground side. If one of those was the issue, it wouldn't start period.
Netural AND kickstand up should be the most "powerful" activation of the system. Starting with only one means it should start with both..... very strange. You're right though, the clutch switch might have not activated just the first time for some reason. If it happens again, don't change anything and just pump the clutch lever a few times. A flakey clutch switch is the most plausible answer right now.