When initiative is not considered, the order you place your ninjas on your team matters too if i remember correctly.
Did you move your main after your other ninjas have been place into their positions?

The order you drag/move your ninjas onto your team,
for example if you drag gai sensei and place him on your team first, then you have moved your lightning main, you'll see gai sensei buffing your team before your main does with lightning enhancement.