Theres more information about Gendun Gyatso here
http://dorjeshugden.com/wp/?p=3101I quote:
Gendun Gyatso (dge ‘dun rgya mtsho) was born in 1475 in the Tanak area of Tsang...His paternal grandfather, a Shangpa Kagyupa named Lama Donyo Gyaltsan, was a disciple of the Sakya patriarch Namkha Naljor and founder of the Sakya monastery Tanak. Donyo Gyaltan’s son, Kunga Gyaltsan, a disciple of Gendun Drup, was Gendun Gyatso’s father. His mother was Kunga Palmo, considered to be a reincarnation of the consort to the Kagyu master Gotsangpa.
It kind of reflects the current Dalai Lamas family where he is the Dalai Lama, his older brother is Taktser Rinpoche and his younger brother is Ngari Rinpoche.
AND there are other instances of such reincarnations teaching reincarnations within the Dorje Shugden lineage. For example, in the Sakya tradition Kunga Lodros grandson Pema Dudul wrote about his grandfather as an emanation of Dorje Shugden himself (
http://truthaboutshugden.wordpress.com/tag/sonam-rinchen/):
Mahasiddha Pema Dudul’s grandfather was Sachen Kunga Lodro, a great leader of the Sakya tradition and the 31st Sakya Throneholder, who was believed to have been an incarnation of Dorje Shugden. Kunga Lodro wrote a wrathful torma offering to Dorje Shugden’s five lineages called Swirl of Perfect Sense Offerings and carried on the tradition of his own father, the 30th Throneholder Dagchen Sonam Rinchen, praising Dorje Shugden as an enlightened protector.
So it goes Kunga Lodro (grandfather) --> Tashi Rinchen (father) --> Pema Dudul (author)
In addition to the above, it is said that Kunga Lodros father Sonam Rinchen composed the ritual to Dorje Shugden and made him well-accepted amongst the Sakyas (
http://dorjeshugden.com/wp/?p=10184):
There are also several short liturgical works on Dorje Shugden written approximately 200 years ago by the Sakyas. This collection of works is known as the Dorje Shugden Be’u Bum. In one part of the Sakya ritual, Requesting to Annihilate Interfering Forces, the name Dorje Shugden was mentioned. As mentioned earlier, Sonam Rinchen is said to have composed this ritual. In the biography of his son, Kunga Lodro, the 31st Sakya Throne Holder, Kunga Lodro asserted that the ritual was written by his father. He added that he received the tranmission of the ritual from his father. It is said that the ritual is performed during the Secret Hayagriva puja.
AND so it goes Sonam Rinchen (great grandfather) --> Kunga Lodro (grandfather) --> Tashi Rinchen (father) --> Pema Dudul (author)