Maybe you're mistaken. From what I've read, you believe that the positioning of the ninjas matter (ie if they are in the first row, second row etc) But that isn't true. The first thing to take into account when deciding who goes first is based on the ninja's position relative to other ninjas in your team. When you look into your Ninja tab, You will see your ninjas having a Position 1, Position 2, Position 3, Position 4 above their name. Between you and your opponent, your Position 2 ninja will never move before your opponent's Position 1 ninja when both of you cast a mystery at the same time. (Unless the mystery is not prompt for your opponent) The only instance initiative comes into play is when both Position 2 ninjas from both you and your opponent decides to use a mystery. This is when having the higher initiative comes into play and you will move first in this instance.

From this, you can see that it doesn't matter whether you have your ninjas being in the second row first position etc or not. Hopefully I understood your problem right, based on how you described it?