What is the problem between the Nyingma and the Gelug?

Although most of my family are Gelugpas who rely on Dorje Shugden, some of them are Nyingmapas. My younger sister married a Nyingmapa Lama from western Tibet from a renowned lineage, he was called Ngora Lama. They had many children, and I visited them frequently, sometimes he and I would do puja together. I would do Dorje Shugden puja and he would do his own practice. We had a very good relationship until his death in Mussourie, India. Now his youngest son and my sister are living in Manjushri Centre in England.

When I lived in Mussourie I had many good friends from the Nyingma tradition, one of whom in particular was called Ngachang Lama. He was an old man, a lay practitioner; one winter he and I did retreat in the same house. In between sessions we talked Dharma, each talking about our experiences. His oldest son would often invite me to his house to do puja. Also, I was often invited to do puja at houses of other Nyingma families. I was so surprised to hear the Dalai Lama and others saying that Dorje Shugden practitioners and Nyingmapa practitioners are like fire and water! (Geshe Kelsang Gyatso, talk.religion.buddhism, 19 December 1997)

Some people believe that if Gelugpa practitioners practice Nyingma teachings, Dorje Shugden will harm them, but this is completely wrong. We never believe this. Impossible. Besides Dorje Shugden, there are many Tibetan stories of other Dharmapalas killing people. There is even a lama called Ra Lotsawa who killed thirteen tantric masters including Tarma Dode, Marpa’s son. This is not just superstition. Many monasteries, maybe including Namgyal Dratsang (His Holiness the Dalai Lama’s private monastery), engage in the practice of Yamantaka that comes from Ra Lotsawa’s instructions. So shouldn’t they stop this practice because Lama Ra Lotsawa was a murderer? This would be meaningless. It is similar with Dorje Shugden, but there is no evidence of Dorje Shugden harming anyone. It is just superstition. For example, if a Gelugpa lama who practices Nyingma teachings has an accident, then some people think, “Oh, this is Dorje Shugden’s fault.” This is stupid. Then they write a book about these things, but this is not real evidence. (Geshe Kelsang Gyatso, An Interview With Geshe Kelsang GyatsoTricycle: the Buddhist Review, No. 27, Spring 1998, p. 76)