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The Finno-Ugric origin was established in a time when Hungary was under strict rule, denied her freedom (after we lost the War of Independence of 1848-49), by two Germans (who learnt Hungarian late in their lives). Now, the national camp claims they served the Austrian court which wanted to break the Hungarian spirit, tearing our roots was one of their way. Up to that point there was little question of our ancestry, leading back to the Scythians and Huns (whom were thought the same anyway), they say with the new theory this chain of continuity and identity was broken. Since Finns and Lapps were some subjugated forest people in some backward shithole far from anything civilized back then many felt this as an insult too.
During the communism, it is undeniable that the Central Committee of the Soviet Union decided everything that happened in the Eastern Block (and therefore at us), they set the tone of the education and historiography as well. The communist chain of command also demanded loyalty and trustworthiness from all who aspired to hold an office (like a cathedra at a uni). The national researchers say after the German influence we fell victim of the Slavic one those times.
All this is usually tied to some Jewish plot too somehow. Right now I'm not sure how that goes.
I wanted to add previously but forgot. All the alternative theories are followed by a specific crowd, whom expect from the lecturers to say certain things, to cater to their expectations. So usually those who fell out from the good grace of the leading strongmen of the academics, for relatively minor deviance from the official line, they have to correct what they say to the new audience, so at least someone hears them out. Making peace with the Scytho-Christian Sirian Shamans is a must.