There are multiple reasons that this may happen. It may be due to the difference in ninja equipment, Treasure Tools, Tactics, etc. I suggest looking at both lineup and their equipment and making sure that the ninjas are using the exact same thing in both lineups. Sometimes one lineup might be missing something the other has equipped. Each lineup is separate from the other, so the changes you make in one lineup, won't always necessarily affect the other.

~Jib

Glad you found the reason xD