There are 27 true runes and every game has to revolve around at least one different true rune, otherwise it would just be repetitive. Its not the bloody triforce or something.
By the way, doesn't Leknaat use her back gate rune to banish the phantom captain thing during the scene with Ted in Suikoden 4? I'm sure she also uses her true rune to project her spirit when she visits the heroes in all the other games. Leknaat seems more human in Suikoden 1 but in the other games she seems kind of ethereal.