The Foundation for the Preservation of the Mahayana Tradition (FMPT) and New Kadampa Tradition (NKT) are both Gelugpa traditions of Mahayana Buddhism,
The original inspiration and guide of the FPMT is its Founder, the late Lama Yeshe. His wish in establishing the FPMT was to spread Buddha’s teachings (Dharma) in the West, a wish that the NKT is also fulfilling. The Founder of the NKT is Venerable Geshe Kelsang Gyatso. There was no conflict between Lama Yeshe’s and Geshe Kelsang’s intentions to spread Mahayana Dharma with the blessings of their Spiritual Guide Vajradhara Trijang Dorjechang (1901-1981), and they were close friends and peers who regularly engaged in Gelugpa spiritual practice together, including monthly Dorje Shugden pujas.
Vajradhara Trijang Rinpoche widely propagated the practice of Wisdom Buddha Dorje Shugden throughout his life. Lama Yeshe engaged in this practice every day, and Lama Zopa, Lama Yeshe’s principal disciple, engaged in the practice until Lama Yeshe passed away in the early 1980s. Originally Lama Zopa had great respect for Geshe Kelsang.
From its side, the NKT has nothing against the FPMT and wishes it well — the more Mahayana Dharma in the world, the better.